From owner-proteins@net.bio.net Tue Dec 01 22:00:00 1992 Path: biosci!uwm.edu!ux1.cso.uiuc.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Newsgroups: bionet.molbio.proteins Subject: Re: Signal sequence prediction Message-ID: Date: 2 Dec 92 22:45:02 GMT References: <1992Dec2.164114.1@uwovax.uwo.ca> Sender: news@usenet.ucs.indiana.edu (USENET News System) Organization: Biology, Indiana University - Bloomington Lines: 111 Nntp-Posting-Host: sunflower.bio.indiana.edu In article <1992Dec2.164114.1@uwovax.uwo.ca> michael@uwovax.uwo.ca writes: >A very long time ago, I got hold of and used a program that could predict >the occurence of consensus signal sequences in protein sequences (called >sig_seq.exe ???). Here is an example of how to search for software when you only know some key words. At the IUBio archive, all of the software readme and help files are index for searching thru gopher. You remember key words like "predict signal sequence". Here is how the modern biologist can go to his electronic library, and search out software titles: Go to the biology software and data library at Indiana U: gopher ftp.bio.indiana.edu 1. About-IUBio-Gopher [21Jun92, 3kb]. 2. About-New-Features [ 1Nov92, 3kb]. 3. Drosophila/ 4. Genbank-Sequences/ --> 5. IUBio-Software+Data/ ... Since you want some software help, look in the software+data section: --> 1. Search IUBio archive ReadMes, Docs & Help files 2. Archive.doc [17Dec91, 16kb]. 3. File listing [11Nov92, 71kb]. 4. New files listing [11Nov92, 12kb]. 5. biology/ ... Since you don't remember the name of the software, try asking the librarian: Search IUBio archive ReadMes, Docs & Help files: signal and sequence and predict Here are the results of that search: 1. 0reviews.txt /bio/archive/molbio/mac/. 2. pm-macinmolbio.txt /bio/archive/molbio/mac/. 3. pcr.help /bio/archive/help/. 4. netgene.server.help /bio/archive/help/. --> 5. soft-dos.help /bio/archive/help/embl/. 6. analyze-signalase.readme /bio/archive/molbio/mac/. I happen to know that the first 2 are long reviews of various software. They are probably worth some of your time to scan thru if you haven't. Item 3 doesn't sound like what we want. Item 4 might or might not help. Item 6 sounds promising, if you have a Macintosh, and item 5 sounds like help from the EMBL archive. Well, looking at item 6, we see: This section is from the document '//IUBio-Software+Data/molbio/mac/analyze-sign alase.readme'. This program is designed for use on the macintosh. It can be decoded using binhex or stuffit. For further information, contact Ned Mantei at BIOCHEMI.CZHETH5A.bitnet. It uses a weight-matrix method to try to predict the site at which signal peptides in secretory peptides are cut off by the signal peptidase. And looking thru item 5, we find this tidbit: filename SIGSEQ.UUE update 11-Dec-1989 version 1.0 size 60 k compressed PAK ASCII conversion UUE author Popowicz A.M. description Prediction of signal sequence cleavage site literature CABIOS 4 (1988), 405-406 source code C sw requirements (Compiler for recompiling) hw requirements - The top of item 5 tells us how to get SIGSEQ.UUE if we want: This section is from the document '//IUBio-Software+Data/help/embl/soft-dos.help '. From NETSERV@EMBL-Heidelberg.DE Fri Sep 6 13:53:45 1991 HELP DOS_SOFTWARE [DIR DOS_SOFTWARE] MS DOS Molecular Biology Software on EMBL File Server ----------------------------------------------------- Molecular biological software for IBM PC and clones is available from the EMBL File Server. Though all programs are tested we can make no warranty on the functionality of these programs nor shall be liable for any damage resulting from their usage. [...] To get any file from the EMBL File Server use normal E-mail addressed to NETSERV@EMBL-Heidelberg.DE. The body of the mail message should contain one server command per line. >Would anyone recall where this is (Archie or the Gopher >don't help with the amount of info I have at the moment!). So it sounds to me like you did have enough info to ask the electronic librarian at Iubio for help. -- Don -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405 From owner-proteins@net.bio.net Tue Dec 01 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!uunet!utcsri!torn!newshost.uwo.ca!uwovax.uwo.ca!michael From: michael@uwovax.uwo.ca Newsgroups: bionet.molbio.proteins Subject: Signal sequence prediction Message-ID: <1992Dec2.164114.1@uwovax.uwo.ca> Date: 2 Dec 92 20:41:14 GMT Sender: news@julian.uwo.ca (USENET News System) Organization: University of Western Ont, London Lines: 10 Nntp-Posting-Host: hydra.uwo.ca A very long time ago, I got hold of and used a program that could predict the occurence of consensus signal sequences in protein sequences (called sig_seq.exe ???). Would anyone recall where this is (Archie or the Gopher don't help with the amount of info I have at the moment!). Many thanks, Michael Clarke Dept. of Microbiology and Immunology University of Western Ontario London, ON N6A 5C1 CANADA From owner-proteins@net.bio.net Tue Dec 01 22:00:00 1992 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Announcements of the Protein Information Resource Message-ID: <01GRUA9XSD4M94DW7D@NBRF.Georgetown.Edu> Date: 2 Dec 92 16:53:52 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 226 Announcements of the Protein Information Resource Network Request Service Highlights 1. Submitting Sequence Data to GenBank, EMBL, DDBJ or PIR 2. PIR Network Request Service Command Summary 1. Submitting Sequence Data to GenBank, EMBL, DDBJ or PIR The National Biomedical Research Foundation Protein Information Resource has a Network Request Server that, among other things, accepts electronic submission of sequence data. Sequence data submission policies have been designed by agreement among the nucleotide and protein sequence databanks. We wish to take this opportunity to restate for BIONEWS subscribers a few general guidelines on submission of their sequence data. Researchers should submit nucleotide sequence data directly to GenBank or EMBL for assignment of an accession number prior to publication. Derived amino acid sequence data may also be included at the same time. Amino acid sequence data submitted in this way to GenBank, EMBL or DDBJ are eventually passed on to PIR, and need not be submitted separately to PIR. This is done so correct cross- references can be made between nucleotide and protein sequence accession numbers. All other amino acid sequences may be submitted directly to PIR when the authors permit their public release prior to publication. Sequences submitted for publication in the journal Protein Science are automatically passed on to the PIR for assignment of accession numbers prior to publication, and those authors do not need not to make separate submissions. Authors are strongly urged to use the sequence submission software package AUTHORIN to submit their sequence data to the databanks; a free copy (for either the IBM PC or Macintosh) can be obtained by sending your request and regular postal mailing address to: authorin@net.bio.net Japanese authors who use the NEC 9801 PC should communicate directly with DDBJ, as these machines use a version of DOS that is significantly different enough to render the discs unreadable on MS-DOS computers here. The staff at DDBJ will forward the data to the appropriate databank via electronic mail. DDBJ may be contacted at: ddbjsubs@flat.nig.ac.jp The address for GenBank submissions is: GenBank Submissions Mail Stop K710 Los Alamos National Laboratory Los Alamos, NM 87545 U.S.A. Telephone: (505) 665-2177 Electronic mail: gb-sub@life.lanl.gov The address for EMBL submissions is: EMBL Data Submissions Postfach 10.2209 D-6900, Heidelburg Federal Republic of Germany Telephone (+49) 6221-387-258 Electronic mail: DATASUBS@EMBL-Heidelberg.DE The address for DDBJ submissions is: DNA Database of Japan Center for Genetic Information Research National Institute of Genetics 111 Yata Mishima, Shizuoka 411 JAPAN Telephone (+81) 559-75-3651 Electronic mail: ddbjsubs@flat.nig.ac.jp The address for PIR submissions is: PIR Submissions National Biomedical Research Foundation 3900 Reservoir Road, NW Washington, DC 20007 U.S.A. Telephone: (202) 687-2121 Electronic mail: FILESERV@GUNBRF.BITNET, FILESERV@NBRF.Georgetown.EDU While we would again urge that AUTHORIN be used as the first choice in data submission tools, the GenBank/EMBL/PIR Data Submission Form can be obtained either by sending a message consisting of the word DATASUB to retrieve@net.bio.net or by sending a message consisting of the words SEND SUBFORM to the FILESERV address. This form can be filled in using any text editor, saved in ASCII (text) format, and mailed electronically or on disk to the databanks. Please, do not submit data either by electronic mail or on disk in files that are formatted for word processing programs. Such files are almost always unreadable except by systems with the same configuration of computer, operating system and word-processing program. For files sent by disk, either DOS or Mac formatted disks can be used but we would prefer receiving regular "double density" disks rather than "high density" disks. Additional information about submitting sequence data to PIR can be obtained by sending the message HELP DEPOSIT to the FILESERV address. 2. PIR Network Request Service Command Summary The National Biomedical Research Foundation Protein Information Resource network request service is a full-function fileserver and database query system. Operating since August 1990 it is capable of handling database queries, sequence searches and sequence submissions, in addition to fileserver requests. To use this server, request commands should be sent to FILESERV@GUNBRF on BITNET or FILESERV@NBRF.Georgetown.EDU on Internet. The server recognizes the following commands sent either in a mail message, or (if the sender is on BITNET) in a command message or a file: Command Action ------- ----------------------------------------------- ACCESSION list entry codes and titles by accession number AND combine QUERY commands with Boolean AND AUTHOR list entry codes and titles by author BASES list accessible databases CROSS list PIR entry codes and titles corresponding to a particular nucleic sequence database entry DEPOSIT deposit entry for database submission END DEPOSIT terminate deposit entry FEATURE list entry codes and titles by feature table entry GENE list entry codes and titles for a gene name GET return entry by entry code HELP return HELP instructions HOST list entry codes and titles by host species INDEX list SENDable files JOURNAL list entry codes and titles by journal citation KEYWORD list entry codes and titles by keyword MEMBER list alignments containing entry code as a member NOT combine QUERY commands with Boolean NOT OR combine QUERY commands with Boolean OR QUERY begin collecting QUERY commands END QUERY terminate collecting commands and execute QUERY QUIT ignore the remaining text (E-mail signature blocks) RETURN change return address for gateway mail SEARCH search for matching sequences by FASTA procedure END SEARCH terminate sequence for searching SEND send file SPECIES list entry codes and titles by species SUGGEST leave suggestion or correction for PIR staff END SUGGEST terminate suggestion text SUPERFAMILY list entry codes and titles by superfamily name TAXONOMY report taxonomy for scientific or common name TITLE list entry codes and titles by title USE set databases, dates or formats to use in limited searches Multiple commands can be sent with one command on each line of a mail message or file. Commands should NOT be sent on the Subject line of a mail message. Receipt of command messages and files will be acknowledged immediately. Mail messages will be acknowledged by return mail. For help in using any of the commands, send a request of the form HELP topic for example HELP SEARCH In addition to the commands, help instructions are also available on the following topics: Custom_Services Databases FTP Gateway_Access Help_en_Espanol Help_en_francais Hints IBM-VM_BITNET On-Line_Access PIR_Distribution VAX-VMS_BITNET Because of network gateway communication protocols, there are limitations on requests sent through gateways. Users not on BITNET or INTERNET who access the server through local or network gateways should read and carefully follow these instructions before sending requests. Only mail message requests (not command messages or files) can be sent through gateways. Because addresses posted on gateway mail do not always work for the return, before you send requests through network gateways it is strongly recommended that you first contact John S. Garavelli (POSTMAST@GUNBRF on BITNET, POSTMASTER@NBRF.Georgetown.EDU on Internet). We will confirm a return address for you and may instruct you to use the RETURN command to ensure that your request output will reach you. It is not usually necessary to do this if you are on BITNET or INTERNET, unless your system employs a local remailer or your mail program applies a nonstandard return address (for example a personal name on the FROM: line). The BITNET network and the network gateways impose strict limits on file size. Poorly posed database queries may result in output so extensive that it could not be returned by network mail. Therefore, an output limit of 1000 lines for each command and 3000 lines for each request is imposed by the PIR server. The DEPOSIT and QUERY commands, and the SEARCH and SUGGEST commands (in their multiline form) must be followed by their respective END commands after the text appearing on the intervening lines. The DEPOSIT command requires, and the SEARCH command optionally uses, parameters that appear on the same line as the command. Because these four commands are so complex, users should obtain and carefully read the help instructions before attempting to use them. The databases available through the PIR Network Server and their abbreviations for code specification are as follows: Abbreviation Database Update Schedule PIR1 PIR Annotated and Classified Entries quarterly PIR2 PIR Preliminary Entries approximately monthly PIR3 PIR Unverified Entries weekly ALN PIR Alignment Entries semiannually NRL_3D Brookhaven Data Bank Sequences quarterly PATCHX MIPS PIR-Supplementary Database quarterly N NBRF Nucleic GB GenBank (TM) as received GBSUP GenBank (TM) as received GBNEW GenBank (TM) New Entries weekly EMBL EMBL as received EMBLSUP EMBL as received In the FASTA output of the SEARCH command the abbreviation for PATCHX is shortened to PATX and NRL_3D is shortened to NR3D; the longer abbreviation should be used to retrieve an entry with the GET command. Not all commands work with all databases; please read the information returned by the command HELP DATABASES. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMASTER@GUNBRF.BITNET POSTMASTER@NBRF.Georgetown.Edu From owner-proteins@net.bio.net Wed Dec 02 22:00:00 1992 Path: biosci!QMS1.LIFE.UIUC.EDU!Dan_Szymanski From: Dan_Szymanski@QMS1.LIFE.UIUC.EDU ("Dan Szymanski") Newsgroups: bionet.molbio.proteins Subject: TCAmechanism Message-ID: <199212040432.AA05780@ux1.cso.uiuc.edu> Date: 4 Dec 92 04:29:44 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 23 Subject: Time:7:59 PM OFFICE MEMO TCAmechanism Date:11/17/92 Do your netters feel held hostage by this TCA crazed maniac that will not accept a simple answer? I hesitated to send the third one, but still haven't got the anwer i'm looking for, so i'll ask a clearer question, one with a little backround and take the plunge: these days i'm studying HMG protein binding to AT rich sequence of dsDNA. southwestern blots of wheat crude HMG fractions show a number of proteins capable of specific binding, all with an AT component. one of them, and probably all of them, make their binding contacts with the minor groove of the AT DNA. so i wonder why is it that this family of proteins are soluable in 2% TCA?(part of the operational def. of HMG proteins) why is this certain chemical reactivity or some other aspect of their fucntion correlated with 2% TCA soluablility? certainly there are a lot of proteins that are sol. in 2% TCA that don't have these characteristics, but i am curious about the mechanism of TCA precipitation. Does it say anything about the proteins? i promise this is the last posting. if there are no replies i will conclude it happens the same way nucleic acid bind to nitrocellulose. the long goodbye, dan From owner-proteins@net.bio.net Wed Dec 02 22:00:00 1992 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!rice From: rice@embl-heidelberg.de (Peter Rice) Newsgroups: bionet.molbio.proteins Subject: Re: Signal sequence prediction Message-ID: <1992Dec3.094018.54431@embl-heidelberg.de> Date: 3 Dec 92 08:40:18 GMT References: <1992Dec2.164114.1@uwovax.uwo.ca> Organization: EMBL, European Molecular Biology Laboratory Lines: 18 In article <1992Dec2.164114.1@uwovax.uwo.ca>, michael@uwovax.uwo.ca writes: > A very long time ago, I got hold of and used a program that could predict > the occurence of consensus signal sequences in protein sequences (called > sig_seq.exe ???). Would anyone recall where this is (Archie or the Gopher > don't help with the amount of info I have at the moment!). On a related topic, does anyone have a copy of the von Heijne signal sequence database available for anonymous ftp? ----------------------------------------------------------------------------- Peter Rice, EMBL | Post: Computer Group | European Molecular Internet: Peter.Rice@EMBL-Heidelberg.DE | Biology Laboratory | Postfach 10-2209 Phone: +49-6221-387247 | W-6900 Heidelberg Fax: +49-6221-387306 | Germany ... and occasionally price@crc.ac.uk ... From owner-proteins@net.bio.net Wed Dec 02 22:00:00 1992 Path: biosci!TRMETU.BITNET!CONSULT1 From: CONSULT1@TRMETU.BITNET (TAYLAN) Newsgroups: bionet.molbio.proteins Subject: NATO ADVANCED STUDY INSTITUTE Message-ID: <9212040649.AA12751@net.bio.net> Date: 4 Dec 92 06:49:48 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 94 Please, distribute to related persons/organizations Preliminary Announcement NATO ADVANCED STUDY INSTITUTE ----------------------------- MOLECULAR ASPECTS OF OXIDATIVE DRUG METABOLIZING ENZYMES AND THEIR SIGNIFICANCE IN ENVIRONMENTAL TOXICOLOGY, CHEMICAL CARCINOGENESIS,AND HEALTH JUNE 20 -- JULY 2 , 1993 KUSADASI-TURKEY ORGANIZED BY: Emel ARINC (TURKEY), Wolfgang KLINGER (GERMANY), John B. SCHENKMAN (USA), John J. STEGEMAN(USA) The primary aim of Institute will be on the recent advances in biochemical, regulatory and molecular aspects of oxidative drug metabolizing enzymes. Mainly cytochrome P450 dependent and Flavin containing monooxygenases will be covered. Significance of these enzymes in genotoxicology, environmental toxicology, chemical car- cinogenesis will be discussed. Therapeutic P450 inhibitors and cytochrome P4501A1 induction in fish and its potential use in bio- chemical monitoring will be considered as special topics of interest. LECTURERS: Richard F. ADDISON (CANADA) Wolfgang KLINGER (GERMANY) Diana ANDERSON (UK) Sergei V. KOTELEVTSEV (RUSSIA) Emel ARINC (TURKEY) David KUPFER (USA) Johannes DOEHMER (GERMANY) Anthony Y.H. LU (USA) Yoshiaki FUJII-KURIYAMA (JAPAN) Franz OESCH (GERMANY) Anders GOKSOYR (NORWAY) Richard M. PHILPOT (USA) John W. GORROD (UK) John B. SCHENKMAN (USA) Helmut GREIM (GERMANY) John J. STEGEMAN (USA) Ernest HODGSON (USA) Hugo Vanden BOSSCHE (BELGIUM) Eric F. JOHNSON (USA) Chung S. YANG (USA) SESSIONS Session I : BIOCHEMISTRY AND MOLECULAR BIOLOGY OF THE MICROSOMAL CYTOCHROME P450 ISOZYMES Session II : FLAVIN CONTAINING MONOOXYGENASES Session III : METABOLISM AND TOXICITY OF DRUGS AND OTHER XENOBIOTICS Session IV : GENOTOXICOLOGY, PREDICTIVE TESTS, CHEMICAL CARCINOGENESIS AND CYTOTOXICITY Session V : THERAPEUTIC AGENTS AND CYTOCHROME P450 Session VI : ECOTOXICOLOGICAL ASPECTS OF CYTOCHROME P450 AND BIOCHEMICAL MONITORING OF AQUATIC POLLUTANTS Lectures, poster sessions, oral presentations and discussions will be held from 9:00 h. to 12.30 h. and from 16.30 h. till 19:00 h. Approximately 75 participants will be admitted. The Institute is located in a five-star KORUMAR Hotel which has its own beach and Con- ference rooms in KUSADASI, on the Aegean Coast. DEADLINE FOR APPLICATION: February 20, 1993 FINANCES: Participants are expected to cover their own travel and living expenses. A limited number of grants covering (part of) these expenses will be available for participants from NATO countries. No registration fee is due. Upon acceptance, a non-refundable deposit of 100 US dollars will be asked. For application forms, write to Dr. Emel ARINC Director of ASI Middle East Technical University ODTU TR 06531 ANKARA-TURKEY Fax: (90) (4) 210 12 79 Telex no: 42761 ODTK TR Tel: (90) (4) 210 10 00 ---> Ext. 3105 For information through E-mail contact Muzaffer TAYLAN CONSULT1@TRMETU.BITNET From owner-proteins@net.bio.net Wed Dec 02 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!uunet!europa.asd.contel.com!darwin.sura.net!lhc!ironic!lowe From: lowe@ironic.nlm.nih.gov (Todd Lowe) Newsgroups: bionet.molbio.proteins Subject: Re: motifs Message-ID: <1992Dec3.071905.16128@nlm.nih.gov> Date: 3 Dec 92 07:19:05 GMT References: <9211251824.AA06428@xibalba.cshl.org> Sender: news@nlm.nih.gov Distribution: bionet Organization: National Library of Medicine, Bethesda Md. USA Lines: 20 In article <9211251824.AA06428@xibalba.cshl.org>, mzhang@XIBALBA.CSHL.ORG (Michael Zhang) writes: |> Is there any protein or DNA sequence motifs database (or collections) available |> in the network? |> -Michael Zhang |> mzhang@cshl.org Prosite, a database containing over 600 characterized sequence motifs can be found here at the National Center for Biotech Information (NCBI) via anonymous ftp (ncbi.nlm.nih.gov). Look in the /repository/prosite subdirectory once logged in. For that matter, we make available most of the other molecular bio databases in /repository (i.e. Genbank, Swissprot, yeast, enzyme, vector, etc). -- Hope you find what you're looking for... Todd Lowe Basic Research Branch, NCBI Nat. Library of Medicine, NIH Bethesda, MD From owner-proteins@net.bio.net Thu Dec 03 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!network.ucsd.edu!dlk From: dlk@chem.ucsd.edu (Daniel R. Knighton) Newsgroups: bionet.molbio.proteins Subject: New cAMP-dependent Protein Kinase Coordinates Summary: Get them now from Brookhaven PDB prerelease area Message-ID: <1fopasINNf3e@network.ucsd.edu> Date: 4 Dec 92 23:24:12 GMT Organization: University of California San Diego, Chemistry Lines: 36 NNTP-Posting-Host: sdchemi3.ucsd.edu To possibly save time or minimize lost time for the potentially many protein kinase researchers basing experiments on coordinates of the so far sole published protein kinase crystal structure, as a representative of the group that solved the structure, I make the following announcement and request: The 2.7-Angstrom X-ray crystallographic model of the recombinant mouse cAMP-dependent protein kinase catalytic subunit complexed with the peptide inhibitor PKI(5-24) has been revised to correct the enzyme sequence correspondence to electron density (sequence register) for residues 55-64 and 308-339. The first segment is part of the conserved protein kinase catalytic domain; the second is not. The corrections do not change the peptide backbone trace and mostly comprise displacement of the sequence one residue to the carboxy terminus along the backbone path in the specified regions. Therefore, if you are currently using coordinates from PDB entry 1CPK or coordinates obtained from UCSD before October, 1992, please get for yourself, or for your colleagues who may not see this post, the corrected coordinates that are now available by anonymous ftp from the Brookhaven Protein Data Bank prerelease directory. The prerelease file is pdb2cpk.ent on pdb.pdb.bnl.gov (130.199.144.1). This file will become entry 2CPK upon distribution of the regular January 15, 1993, PDB release. If you are not able to get the file from pdb.pdb.bnl.gov for whatever reason, please by all means contact me, and I will e-mail the file to you. Thank you. Daniel Knighton -- Daniel R. Knighton Internet: dlk@chem.ucsd.edu BITNET: dknighto@UCSD FAX: 001-619-534-8193 Mail Code 0654, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0654, U.S.A. From owner-proteins@net.bio.net Fri Dec 04 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!elroy.jpl.nasa.gov!news.claremont.edu!nntp-server.caltech.edu!robin From: robin@cco.caltech.edu (Robert C. Colgrove) Newsgroups: bionet.molbio.proteins Subject: Tyler Jacks and Frameshifting Message-ID: <1fpd0cINNa73@gap.caltech.edu> Date: 5 Dec 92 04:59:56 GMT Organization: California Institute of Technology, Pasadena Lines: 34 NNTP-Posting-Host: alumni.caltech.edu E85J000 writes: >Has anyone out there seen any recent articles from Tyler Jacks since >hisoriginal work with ribosomal frameshifting in RSV's gag-poL? I >haven't been able to find anything since the Cell 55(447-458) paper >in 1988 on the signals for frameshifting. I've been doing a lot of >work recently on a term paper on the subject and haven't been able to >find anything, though his work up to '88 seems top notch. I'm sure Tyler would be tickled to get such a glowing endorsement! Tyler was a fellow grad stud at UCSF in the mid-80's in biochem. Truly a star, he did indeed nail the frameshifting problem -what was then called the gag-pol problem pretty well-. Anyway, he graduated and is now a postdoc at the whitehead. He doesn't work on frameshifting anymore (has been hard at work on an RB-knockout mouse). We collaborated at the time on a massive and essentially negative search of genbank for likely shifty sequences. If you have any specific questions, you could try phoning the Whitehead or I could forward them. Historical tidbit: Tyler demonstrated framshifting first in RSV gagpol. When I wrote a program to search Genbank for similar Motifs, it found all the then-known shifters EXCEPT RSV itself! Curious, I checked the header info (which the program used to create a virtual cDNA sequence) and found that the authors (Gilbert and co.) had put in an intron ad hoc to "explain" how gagpol got made. This misinformation so far as I know still sits in GenBank along with god knows how many others weird errors accumulated like cybernetic sediment in the database. Caveat Searchor... I told tyler last year to get on the net but flattery was not one of the expected benefits...;^). hope this helps robin colgrove fellow in infectious diseases harvard medical school robin@calypso.bih.harvard.edu From owner-proteins@net.bio.net Fri Dec 04 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!uunet!elroy.jpl.nasa.gov!news.claremont.edu!nntp-server.caltech.edu!robin From: robin@cco.caltech.edu (Robert C. Colgrove) Newsgroups: bionet.molbio.proteins Subject: signal sequence prediction Summary: I have it but it's deeply buried... Keywords: signal sequence, Von Heijne Message-ID: <1fpdkmINNae2@gap.caltech.edu> Date: 5 Dec 92 05:10:46 GMT Organization: California Institute of Technology, Pasadena Lines: 14 NNTP-Posting-Host: alumni.caltech.edu Several asked about signal sequence prediction. When the Von Heijne paper came out when i was in grad school, I wrote some c programs to implement it, plot it and do cute stuff like sort all of genbank for good looking signals. I presume that this is all archaic by now and that much more professional stuff is online somewhere, but if not I could rummage through my old disks and email the sections of my thesis that have the Von Heijne matrix, a c program to use it and some unix scripts to plot the results. Would take a bit of work, though. Let me know if this would be helpful (like i said, i suspect "real" programmers have written and archived better stuff elsewhere) robin@calypso.bih.harvard.edu From owner-proteins@net.bio.net Sun Dec 06 22:00:00 1992 Path: biosci!agate!spool.mu.edu!think.com!enterpoop.mit.edu!bloom-picayune.mit.edu!athena.mit.edu!retentiv From: retentiv@athena.mit.edu (Sandra Chang) Newsgroups: bionet.molbio.proteins Subject: Re: Tyler Jacks and Frameshifting Message-ID: <1992Dec7.140840.27057@athena.mit.edu> Date: 7 Dec 92 14:08:40 GMT References: <1fpd0cINNa73@gap.caltech.edu> Sender: news@athena.mit.edu (News system) Organization: Massachusetts Institute of Technology Lines: 22 Nntp-Posting-Host: carbonara.mit.edu In article <1fpd0cINNa73@gap.caltech.edu> robin@cco.caltech.edu (Robert C. Colgrove) writes: > >E85J000 writes: > >>Has anyone out there seen any recent articles from Tyler Jacks since >>hisoriginal work with ribosomal frameshifting in RSV's gag-poL? I >called the gag-pol problem pretty well-. Anyway, he graduated and is >now a postdoc at the whitehead. He doesn't work on frameshifting anymore >(has been hard at work on an RB-knockout mouse). We collaborated at the >hope this helps >robin colgrove >fellow in infectious diseases >harvard medical school >robin@calypso.bih.harvard.edu In case someone is trying to track him down, Tyler is now at MIT's Center for Cancer Research, starting up his own lab there. His focus is pretty much on knockout mice it seems. john travis From owner-proteins@net.bio.net Sun Dec 06 22:00:00 1992 Path: biosci!uwm.edu!caen!uunet!utcsri!utzoo!zhiwei From: zhiwei@zoo.toronto.edu (Zhiwei Wang) Newsgroups: bionet.molbio.proteins Subject: protein kinase C Message-ID: Date: 7 Dec 92 19:48:43 GMT Organization: U of Toronto Zoology Lines: 7 Do anybody have experience using ProMega non-radioactive protein kinase C assay kit to quantity the enzyme, especially by spectrophotometric method? I followed the instruction precisely but got very low absorbance readings. Any comments welcome. Zhiwei Wang U of T Canada From owner-proteins@net.bio.net Sun Dec 06 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.general,bionet.molbio.proteins,bionet.software Subject: NRL_3D Available for searching via Gopher Message-ID: <1992Dec7.202401.7417@welchgate.welch.jhu.edu> Date: 7 Dec 92 20:24:01 GMT Organization: Johns Hopkins Univ. Welch Medical Library Lines: 241 Xref: biosci bionet.general:3718 bionet.molbio.proteins:453 bionet.software:3730 The NRL_3D database is now available for searching by gopher. ================================================================ Description of NRL_3D From the NRL_3D documentation: NRL_3D is a protein sequence--structure database derived from the high resolution X-ray structures of proteins deposited in the Brookhaven National Laboratory's Protein Data Bank (PDB) (1) as of October 1988. NRL_3D has been conceived, developed, and tested by K. Namboodiri, N. Pattabiraman, A. Lowrey, and B. Gaber (2, 4) at the Naval Research Laboratory, Washington, D.C., and incorporated into the Protein Identification Resource (PIR) (3) by D. George and W. C. Barker at the National Biomedical Research Foundation, Washington, D.C. When citing this work please refer to references 2, 3, and 4. The PDB contains the atomic coordinates for the three-dimensional structure of a number of proteins obtained using single crystal X-ray diffraction data or other methods. One often would like to select sets or subsets of coordinate data according to sequence properties. However, the primary sequence information in the PDB is not represented in a form that is compatible with the sequence manipulation programs of the PIR or other sequence analysis software packages. The NRL_3D database provides a link between this software and the PDB and allows the sequence portion of the PDB to be searched and analyzed. Sequence data from selected coordinate sets in the PDB were extracted and reformatted in an NBRF-like format (see the PIR Document Database File Structure and Format Specification for details). These data have been set up as a database and are fully accessible to all of the PIR programs. Coordinate sets were selected on the criteria that 1) they corresponded to well-defined protein sequences, 2) they were determined with resolutions of 3.0 Angstroms or less, and 3) they were not determined by molecular mechanics or other theoretical techniques. When a selected PDB entry contained more than one polypeptide chain, each chain was represented as a separate entry in NRL_3D. In addition, if more than 3.8 Angstroms separated the alpha-carbons of adjacent amino acids, the sequence was divided into separate fragments and each fragment was represented in a separate entry. Large separations between adjacent amino acids result when an intervening sequence fragment cannot be resolved in the electron density map; the existence of large separations indicates that the sequence is not complete or that the chains are not covalently connected. (....) References ---------- 1. Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F., and Weng, J. (1987) in Crystallographic Databases - Information Content, Software Systems, Scientific Applications, eds., Allen, F.H., Bergerhoff, G., and Sievers, R., Data Commission of the Int'l Union of Crystallography, Bonn, Cambridge, Chester, pp. 107-132. 2. Namboodiri, K., Pattabiraman, N., Lowrey, A., and Gaber, B.P. (1988) Automated Protein Structure Data Bank Similarity Searches and Their Use in Molecular Modeling with MIDAS, J. Mol. Graphics 6, 211-212. 3. George, D.G., Barker, W.C., and Hunt, L.T. (1986) The Protein Identification Resource (PIR), Nucl. Acids Res. 14, 11-15. 4. Pattabiraman, N., Namboodiri, K., Lowrey, A., and Gaber, B.P. (1989) Protein Sequences & Data Analysis (communicated). ============================ A typical entry is as follows: ENTRY 1ACE1 #Type Protein (fragment) TITLE Acetylcholinesterase, fragment 1 - Torpedo californica (electric ray) #EC-number 3.1.1.7 COMMENT PDB code: 1ACE SOURCE Torpedo californica #Common-name electric ray REFERENCE #Authors Sussman J.L., Harel M., Silman I. #Citation coordinates deposited in Brookhaven National Laboratory's Protein Data Bank REFERENCE #Authors Sussman J.L., Harel M., Frolow F., Oefner C., Goldman A., Toker L., Silman I. #Journal Science (1991) 253:872 #Title Atomic structure of acetylcholinesterase from torpedo californica: a prototypic acetylcholine-Binding protein. REFERENCE #Authors Sussman J., Harel M., Frolow F., Oefner C., Toker L., Silman I. #Book Cholinesterases: Structure, Function, Mechanism, Genetics, and Cell Biology, Massoulie, J., Bacou, F., Barnard, E., Chatonnet, A., Doctor, B., and Quinn, D.M., eds., pp.7, American Chemical Society, Columbus, Oh, 1991 #Title Structural studies on acetylcholinesterases from torpedo californica. REFERENCE #Authors Sussman J.L., Harel M., Frolow F., Goldman A., Oefner C., Toker L., Silman I. #Journal Proceedings Of The 1991 Medical Defense Bioscience Review (1991) 0:441 #Title 3-D structure of acetylcholinesterase from torpedo californica. REFERENCE #Authors Sussman J.L., Harel M., Frolow F., Silman I. #Journal Proceedings Of The 1989 Medical Defense Bioscience Review (1989) 0:309 #Title X-ray crystallographic studies of acetylcholinesterase. REFERENCE #Authors Sussman J.L., Harel M., Frolow F., Varon L., Toker L., Futerman A.H., Silman I. #Journal J. Mol. Biol. (1988) 203:821 #Title Purification and crystallization of a dimeric form of acetylcholinesterase from torpedo californica subsequent to solubilization with phosphatidylinositol-specific phospholipase c. COMMENT Resolution: 2.8 angstroms COMMENT R-value: 0.186 COMMENT Determination: X-ray diffraction KEYWORDS Hydrolase(carboxylic esterase) FEATURE 76-80 #Region helix (right hand alpha)\ 130-137 #Region helix (right hand alpha)\ 165-181 #Region helix (right hand alpha)\ 198-208 #Region helix (right hand alpha)\ 235-248 #Region helix (right hand alpha)\ 256-265 #Region helix (right hand alpha)\ 268-275 #Region helix (right hand alpha)\ 301-308 #Region helix (right hand alpha)\ 325-332 #Region helix (right hand alpha)\ 346-356 #Region helix (right hand alpha)\ 362-372 #Region helix (right hand alpha)\ 381-408 #Region helix (right hand alpha)\ 457-476 #Region helix (right hand alpha)\ 3-7,10-17,24-28,93-99, 138-144,107-113, 190-196,218-223, 314-321,413-420 #Region beta sheet\ 64-91 #Disulfide-bonds\ 251-262 #Disulfide-bonds\ 399 #Disulfide-bonds interchain (to 1ACE2:32)\ 197,324,437 #Site SUMMARY #Length 481 #Checksum 6848 SEQUENCE 5 10 15 20 25 30 1 S E L L V N T K S G K V M G T R V P V L S S H I S A F L G I 31 P F A E P P V G N M R F R R P E P K K P W S G V W N A S T Y 61 P N N C Q Q Y V D E Q F P G F S G S E M W N P N R E M S E D 91 C L Y L N I W V P S P R P K S T T V M V W I Y G G G F Y S G 121 S S T L D V Y N G K Y L A Y T E E V V L V S L S Y R V G A F 151 G F L A L H G S Q E A P G N V G L L D Q R M A L Q W V H D N From owner-proteins@net.bio.net Wed Dec 09 22:00:00 1992 Path: biosci!agate!spool.mu.edu!sol.ctr.columbia.edu!destroyer!cs.ubc.ca!unixg.ubc.ca!otter.biochem.ubc.ca!logan From: logan@otter.biochem.ubc.ca (Logan Donaldson) Newsgroups: bionet.molbio.proteins Subject: simple display software for pc's Message-ID: <1g8uljINNo1e@iskut.ucs.ubc.ca> Date: 11 Dec 92 02:33:23 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 8 NNTP-Posting-Host: otter.biochem.ubc.ca Greetings! I am looking for an inexpensive (shareware, even better) program that will display molecular models in wire-frame, ball'n'stick and space- filling representations for the ibm-pc. Something like MacMolecule would be great! Thanks! Logan Donaldson From owner-proteins@net.bio.net Wed Dec 09 22:00:00 1992 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!zaphod.mps.ohio-state.edu!moe.ksu.ksu.edu!crcnis1.unl.edu!wupost!waikato.ac.nz!comp.vuw.ac.nz!am.dsir.govt.nz!chv.lincoln.cri.nz From: srckuxw@chv.lincoln.cri.nz Newsgroups: bionet.molbio.proteins Subject: gamma Glutamyl transpeptidase. Message-ID: <2b289bfc.3936@chv.lincoln.cri.nz> Date: 11 Dec 92 00:47:40 GMT Organization: Canty Agriculture & Science Centre Lines: 6 hello folks, I'm working with gamma glutamyl transpeptidase and I'm looking for a detection method after SDS Gel electrophoresis . Does anybody know of any antibody or other methods available? Thanks. Martin. From owner-proteins@net.bio.net Thu Dec 10 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!uunet!spool.mu.edu!caen!destroyer!cs.ubc.ca!unixg.ubc.ca!otter.biochem.ubc.ca!logan From: logan@otter.biochem.ubc.ca (Logan Donaldson) Newsgroups: bionet.molbio.proteins Subject: simple display software for pc's Message-ID: <1g98afINNot1@iskut.ucs.ubc.ca> Date: 11 Dec 92 05:18:07 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 8 NNTP-Posting-Host: otter.biochem.ubc.ca Greetings! I am looking for an inexpensive (shareware, even better) program that will display molecular models in wire-frame, ball'n'stick and space- filling representations for the ibm-pc. Something like MacMolecule would be great! Thanks! From owner-proteins@net.bio.net Thu Dec 10 22:00:00 1992 Path: biosci!MACC.WISC.EDU!HXIE From: HXIE@MACC.WISC.EDU (HUIWEN XIE) Newsgroups: bionet.molbio.proteins Subject: off Message-ID: <22121123532135@vms2.macc.wisc.edu> Date: 12 Dec 92 04:53:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 1 Please sign me off. Thanks. From owner-proteins@net.bio.net Thu Dec 10 22:00:00 1992 Path: biosci!uwm.edu!psuvax1!atlantis.psu.edu!wintermute.phys.psu.edu!ra!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.proteins Subject: Re: simple display software for pc's Message-ID: <1992Dec11.163303.145@welchgate.welch.jhu.edu> Date: 11 Dec 92 16:33:03 GMT References: <1g8uljINNo1e@iskut.ucs.ubc.ca> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 148 In article <1g8uljINNo1e@iskut.ucs.ubc.ca> logan@otter.biochem.ubc.ca (Logan Donaldson) writes: >Greetings! I am looking for an inexpensive (shareware, even better) program >that will display molecular models in wire-frame, ball'n'stick and space- >filling representations for the ibm-pc. > >Something like MacMolecule would be great! > > There was a discussion about this last summer - there are pros and cons to using a PC for this type of work - much depends on what you want to do (but that's another discussion :-). Eric Hugo of Wash U. St. Louis posted the follwoing summary about the responses to his (similar) question. This article was retrieved from Don Gilbert's Gopher hole's search index of biosci articles (kudoes to Don). Regards, Dan Jacobson danj@welchgate.welch.jhu.edu ================================================================================ Of the answers I received one set of programs was mentioned that is available by anonymous ftp. These are shareware programs written at the University of Illinois and distributed by Dr. A.R Croft. These programs (pdViewer and PSAAM) are written in Visual Basic and run under Windows 3.x. I've just downloaded them and am in the process of evaluating them. The two programs can be obtained from nemo.life.uiuc.edu (128.174.183.6) in the pub/pdvwin and the pub/psaam subdirectories by anonymous ftp. Thanks to all of the individuals that responded to my query, the information was greatly appreciated. Eric ;-) SUMMARY INFORMATION: Tom Branham writes: I do know of a commercial program called HyperChem from Autodesk for which the educational price is $600, but they do have a full free to researchers program (if you keep them updated on your work, etc.) The program is not only a visual interface, but performs molecular orbital calculations and molecular dynamics. I have been very tempted to take them up on the research program, but the one thing worrying me is that it comes with a hardware key and I have serial ports that are not well behaved. If anyone else comes up with any other sugestions I would appreciate hearing about them, as I am running Quanta at the lab, on our SGI's, and then I am working with my own programs, lotus123 and Mathcad at home on the pdb files, but can not view them at home, a minor irritation. I also purchase the programs on my own rather than with lab moneys. I like to feel that I do not "live off " the lab grants, perhaps a sense of hubris I REally can not afford this month :) ........Tom Branham P. S. Dr. Pochapsky brought back the PDB and Atlas of sequences from the same meeting. Wasn't that a Nice suprise.....? Watson Ko writes: Alchemy III will do the job you want, but it will be very slow if you try to rotate(or whatever) since the program has to redraw the whole molecule. What I did was just showing the active site of the specific enzyme(or protein) and manipulated the molecule. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Watson Ko v999r36x@ubvms.cc.buffalo.edu Space, the final ... parking place! =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Jim Cassatt writes: I have been using a shareware version of PCMODEL. Check previous messages regarding availability. Included are two sample files for chymotrypsin and B-DNA obtained from the PDB. They can be viewed quite effectively with a 486, less so with a 386SX and poorly with an 8088. What I have not been able to find out is whether a program to convert PDB format to PCMODEL format is available. The main difficulty is generating a connect table. There are also two versions of PCMODET, one a shareware version and the other distributed by Gilbert at Indiana. His version does not have a conversion program. I awaiting a response from the author of the shareware program. Jim Cassatt Dr. Ferenc Czegledy writes: There are several ways that I know of to visualize PDB files in the MS-DOS environment: >>>1. Using pdViewer which one can obtained by anonymous ftp from >>>nemo.life.uiuc.edu >>>The package must be transferred using the binary protocol and runs >>>under Windows 3.1/3.0. 2. Using a package called Alchemy III (for Windows) which is available from Tripos Assoc. Inc. ,St. Louis, MO. Phone: 314-647-1099. 3. Using Chem-X from Chemical Design Inc., 200 Route 17 South, Suite 120, Mahwah, NJ 07430. phone: 201-529-3323. I have only seen the brochure for this package but it looks very impressive. The only problem is that it is very expensive: ~ $ 2,500.00/year. The software will self-destruct after 1 year but if you pay for an additional year the software is upgraded for you. Anyway, good luck and tell me if you hear of any additional approaches to visualization and modeling on the PC. -- Ferenc Czegledy Dept. Of Cardiology Columbia University 630 W 168th Street New York, NY 10032 email: ferenc@cucrd0.med.columbia.edu Rhee Hwan-Seok writes concerning the program MOBY The following is the snail-mail address of MOBY manufacturer. In my address file they have no e-mail address known. ---------------------------- Springer-Verlag Heidelberger Platz 3 W-1000 Berlin 33 F.R.G ( Germany ) Telex : 461723 Telefax : (06221)413982 ---------------------------- They will send you a demo disk FREE of charge. And the disk could be 3" or 5" on your request. e-mail : hyunerho@krsnucc1.BITNET -- Eric R. Hugo, Postdoctoral Research Associate |eric@bcserv.wustl.edu Dept. of Biochemistry and Molecular Biophysics| Washington University School of Medicine | Box 8231, St. Louis, MO 63110_________________| (314) 362-3342 From owner-proteins@net.bio.net Fri Dec 11 22:00:00 1992 Path: biosci!news.cs.indiana.edu!ux1.cso.uiuc.edu!uwm.edu!zaphod.mps.ohio-state.edu!news.acns.nwu.edu!uicvm.uic.edu!u53077 From: U53077@uicvm.uic.edu (Dong Li 312-996-0509) Newsgroups: bionet.software,bionet.molbio.proteins Subject: Help wanted: alignment program for proteins Message-ID: <92346.200424U53077@uicvm.uic.edu> Date: 12 Dec 92 02:04:24 GMT Organization: University of Illinois at Chicago Lines: 21 Xref: biosci bionet.software:3761 bionet.molbio.proteins:459 Dear netters, I am looking for a better alignment program for the alignments of 60 different proteins at same time. The program I am using now can line up only 16 proteins at same time, and I have to divide all 60 proteins into 4 groups to line them up separately, then line the 4 groups up by hands. It is laborious and easy to make mistakes. I would be very grateful if you provide any information about it (or just tell me the site and dir. name so that I can FTP it.) Thank you very much for attention. ************************************************************************* With malice toward none, with charity for all.......... Abraham Lincoln ------------------------------------------------------------------------- Dong Li Telephone: (312) 996-0509 Fax: (312) 413-2435 Internet: u53077@uicvm.uic.edu Bitnet: u53077@uicvm.bitnet Dept. Biological Sciences, Univ. Illinois at Chicago, Chicago, IL 60680 ************************************************************************* From owner-proteins@net.bio.net Fri Dec 11 22:00:00 1992 Path: biosci!daresbury!doc.ic.ac.uk!agate!ames!saimiri.primate.wisc.edu!usenet.coe.montana.edu!news.u.washington.edu!provolone.bchem.washington.edu!merritt From: merritt@provolone.bchem.washington.edu (Ethan A Merritt) Newsgroups: bionet.molbio.proteins Subject: Re: simple display software for pc's Message-ID: <1992Dec11.232815.5903@u.washington.edu> Date: 11 Dec 92 23:28:15 GMT References: <1g8uljINNo1e@iskut.ucs.ubc.ca> <1992Dec11.163303.145@welchgate.welch.jhu.edu> Sender: news@u.washington.edu (USENET News System) Reply-To: merritt@u.washington.edu Organization: University of Washington Lines: 24 In article <1g8uljINNo1e@iskut.ucs.ubc.ca> logan@otter.biochem.ubc.ca (Logan Donaldson) writes: >Greetings! I am looking for an inexpensive (shareware, even better) program >that will display molecular models in wire-frame, ball'n'stick and space- >filling representations for the ibm-pc. > >Something like MacMolecule would be great! I was very impressed by a demonstration of Jane Richardson's Kinemage (sp?) program, currently being distributed as part of what you receive with a subscription to the journal Protein Science. Diskettes with coordinates for relevant proteins come with the journal issue, so it permits the reader to view protein structures described in the articles in more detail and with much more flexibility than would be available using printed figures. The instructions to the authors cover how to generate Kinemage files from normal PDB coords, so I suppose one could use it as a viewer totally independent of the journal as well. I don't know what happens to Kinemage diskettes belonging to library copies of Portein Science - maybe you should ask if your library has kept them to check out with the journal? regards, Ethan A Merritt merritt@u.washington.edu From owner-proteins@net.bio.net Sat Dec 12 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!wupost!spool.mu.edu!yale.edu!jvnc.net!netnews.upenn.edu!phuong From: phuong@chestnut.chem.upenn.edu (Phuong Vi) Newsgroups: bionet.molbio.proteins Subject: thinning the integral membrane of bacteriorhodosin Message-ID: <101858@netnews.upenn.edu> Date: 13 Dec 92 18:58:38 GMT Sender: news@netnews.upenn.edu Organization: NMR Biochemistry Graduate Research Lab Lines: 2 Nntp-Posting-Host: chestnut.chem.upenn.edu I am looking for the ways by which the secondary and tertiary structure of the integral membrane protein could adapt to a thinning of the hydrocarbon core of the host lipid bilayers and relative to that of the normal purple bacteria membrane. Any reference or suggestion will be greatly appreciated..Email please.. From owner-proteins@net.bio.net Sun Dec 13 22:00:00 1992 Path: biosci!daresbury!daresbury!not-for-mail From: mbthm@s-crim1.dl.ac.uk (T.H.L. Murcott) Newsgroups: bionet.software,bionet.molbio.proteins Subject: Re: Help wanted: alignment program for proteins Message-ID: <1gi43tINN31o@s-crim1.dl.ac.uk> Date: 14 Dec 92 14:01:33 GMT References: <92346.200424U53077@uicvm.uic.edu> Distribution: bionet Organization: Daresbury Lab., Warrington, U.K. Lines: 38 Xref: biosci bionet.software:3776 bionet.molbio.proteins:462 NNTP-Posting-Host: seqnet.dl.ac.uk In article <92346.200424U53077@uicvm.uic.edu> Dong Li 312-996-0509 writes: >Dear netters, > >I am looking for a better alignment program for the alignments of >60 different proteins at same time. >The program I am using now can line up only >16 proteins at same time, and I have to divide all 60 proteins into >4 groups to line them up separately, then line the 4 groups up by >hands. It is laborious and easy to make mistakes. > >I would be very grateful if you provide any information about it >(or just tell me the site and dir. name so that I can FTP it.) > >Thank you very much for attention. > >************************************************************************* >With malice toward none, with charity for all.......... Abraham Lincoln >------------------------------------------------------------------------- > Dong Li Telephone: (312) 996-0509 Fax: (312) 413-2435 > Internet: u53077@uicvm.uic.edu Bitnet: u53077@uicvm.bitnet >Dept. Biological Sciences, Univ. Illinois at Chicago, Chicago, IL 60680 >************************************************************************* I have had alot of success with clustal V (five) which can certainly cope with more than 16 sequences at a time. It is available by anonymous ftp from the major molecular biology ftp sites. I would go and find out the details of sitename and directory but I am a novice at UNIX and rn and am pretty sure that I would not be able to get back to your message again to reply!! Good hunting Toby "I dont understand unix but I can spell potato". Toby Murcott Murcott@uk.ac.bristol.bsa Dept. of Biochemistry University of Bristol UK. From owner-proteins@net.bio.net Sun Dec 13 22:00:00 1992 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!caen!destroyer!cs.ubc.ca!unixg.ubc.ca!otter.biochem.ubc.ca!logan From: logan@otter.biochem.ubc.ca (Logan Donaldson) Newsgroups: bionet.molbio.proteins Subject: re: alignment programs Message-ID: <1gipjaINNf1s@iskut.ucs.ubc.ca> Date: 14 Dec 92 20:08:10 GMT Organization: University of British Columbia, Vancouver, B.C., Canada Lines: 58 NNTP-Posting-Host: otter.biochem.ubc.ca The program, seqsee, from the U. of Alberta can perform alignments to the entire protein database or a subset of sequences. It'll also do structure prediction, pattern searches ... and more. An excerpt from the help file is enclosed at the end of this posting. BTW, thanks* for all the suggestions regarding my request for pc display software. I have a copy of pdviewer and I'm currently previewing moby. --Logan Donaldson * Dan Jacobson danj@welchgate.welch.jhu.edu * Lenny Bloksberg pressj@clvax.cl.msu.edu * Adam Godzik adam@scripps.edu * Ethan Merritt merritt@uwashington.edu * ?? czj@cu.nih.gov -------------------------------------------------------------- The programs, databases and libraries contained within SEQSEE have been under continuing development since June of 1988 in the labs of both Frederic M. Richards of Yale University (New Haven) and Brian D. Sykes of the University of Alberta (Edmonton). The SEQSEE project was completed in partial fulfillment of the requirements for the degree of Doctor of Philosophy for David Wishart (Yale, 1991). The principal programmer for SEQSEE has been Robert Boyko with database development and general program design being handled by David Wishart. Funding for this project has been provided in part by Yale University, the Natural Sciences and Engineering Research Council of Canada, the Medical Research Council of Canada and by the Protein Engineering Networks Centre of Excellence (Canada). The complete SEQSEE suite of programs may be freely used by individuals in academic institutions wishing to conduct research or perform database inquiries provided that suitable acknowledgment of both the program and its authors is given. Neither SEQSEE nor portions of the program contained within SEQSEE may be altered, incorporated into other programs or sold for profit by others without express written consent from the authors. For further inquiries about SEQSEE please contact: David Wishart / Robert Boyko Department of Biochemistry University of Alberta Edmonton, Alberta, Canada T6G 2H7 Phone: (403) 492-7797 e-mail: dsw@rigel.biochem.ualberta.ca rbo@sirius.biochem.ualberta.ca --------------------------------------------------------------------- From owner-proteins@net.bio.net Tue Dec 15 22:00:00 1992 Path: biosci!SALK-SC2.SDSC.EDU!mangalam From: mangalam@SALK-SC2.SDSC.EDU Newsgroups: bionet.molbio.proteins Subject: Amino Acid Relationships (long) Message-ID: <9212162113.AA25053@salk-sgi.sdsc.edu> Date: 16 Dec 92 21:13:25 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 243 Saludos Netlandos, I recently asked for pointers or comments about representing the relationships among amino aacids in different ways. (My apologies for cannibalizing text from previous direct replies and the extreme latency in summarizing). Perhaps I was being a little too vague in my original posting, but I wanted as many "alternatives" as possible. I was actually looking for 2 things. I was originally looking for a way of coding substitution matrix probabilities (originally Dayhoff's PAM matrix, but willing to consider others) in a more convenient, compact way for attempting to do sequence comparisons and alignments (more or less the same thing) using digital signal processing techniques. (Any comments, helpfully derogatory or otherwise on such an attempt are also welcome.) The second is related - a way to show in 3-D, using color, transparency, and/or "time-smearing" if neccessary to address other dimensions, some way of representing as many of the characteristics of the amino acids as possible. It occurred to me that it would be a great teaching tool to be able to have as much information coded into a single image as possible (shades of Edward Tufte), and so the impetus to check the net to see how others had approached the problem. I guess the ideal representation for the sequence anlaysis would include a 3D (or 4D or 5D, real or imaginary) vector for each amino acid, the coordinates representing various information about its biochemical nature and substitution frequency (perhaps under different conditions or in different types of protein). That's the ideal. I'll be settling for something less. So, in (just slightly over) 25 words 8), that's what I was fishing for. The fish: -------------- Tom (alternatively "Cassandra" or "what good is it if my computer can't parse it?!" 8-) Schneider of NCI (toms@ncifcrf.gov) has approached the problem with his "sequence logos"; (parsable) reference follows: @article{Schneider.Stephens.Logo, author = "T. D. Schneider and R. M. Stephens", title = "Sequence Logos: A New Way to Display Consensus Sequences", journal = "Nucl. Acids Res.", volume = "18", pages = "6097-6100", year = "1990"} This paper describes a new way to show consensus sequences by changing the size and other attributes of the letters in a consensus sequence to show which residues are represented most. It's a bit startling to view, but it does get the point across and it is certainly easier to pick out homologies than looking at the usual stacked letters of slightly different shading. It is a somewhat "lossy" representation, in that it does not allow you to reconstruct the original sequences, but in many cases that's not a disadvantage. He writes: "To see what they are like, you can look into my anonymous ftp archive at ncifcrf.gov in pub/delila. There is a README with general directions, but the file globin.logo.Z is in PostScript ready to dump to your printer. (.Z means it is compressed. Remember to transfer in binary mode and then uncompress under unix. Tell me if you have trouble with this.) The logo paper itself is also in the archive, as logo.bbl.Z and logo.tex.Z. I could put the PostScript version there if you can't use LaTeX. The four figures are: globin.logo.Z lambcro.logo.Z ribo.logo.Z t7.logo.Z ." Cliff Pickover (cliff@watson.ibm.com) has some wonderful books out (Christmas time is coming up - leave a few hints around) that deal with alternative representations of data ("Computers and the Imagination", "Computers, Pattern, Chaos, and Beauty" [obviously referring to my desk], and most recently "Mazes for the Mind: Computers and the Unexpected") and he recently wrote a paper that tangentially dealt with this problem (non-parsably, DNA and protein tetragrams: biological sequences as tetrahedral movements, J Molecular Graphics 10(March):2-16, 1992) by trying to visualize sequences as 3D movements. For proteins, he tried coding the amino acids as the standard polar/nonpolar/ charged/noncharged as the 4 vectors but also as a dodecahedron (20 points). This latter attempt is closer to what I had in mind, but it still does not correctly address the substitution problem. Distorting the regular dodecahedron brings it closer to what I had in mind and coloration could bring it still closer, but it's still not perfect. As usual, though, Cliff's approach is very good - we've got access to all these tremendously powerful, 3D-capable workstations, but very few techniques have been presented that make use of them to help reduce the data to a more understandable image. His idea of 3D sequence alignments are a nice step in bringing another level of analysis to sequence bashing. Cliff is editing another book coming out Real Soon Now, "The Visual Display of Biological Information" (has a Tufte-ian ring to it doesn't it?), which deals with a number of ways to represent and analyze sequence data (including a bit on Tom's Sequence Logos - see above). Watch for it. Craig Livingstone (cdl@biochemistry.oxford.ac.uk) suggested a paper about different ways to picture the relationships among amino acids. (William R Taylor (1986) The classification of amino acid conservation. J. Theoretical Biology 119:205-218) It's a bit old, but I'm ashamed that I hadn't seen it before - it's one of those rare papers that's a truly _fun_ read - well written and informative, with a number of models presented, warts and all. Also some very nice graphical depictions of said relationships, including some Venn diagrams that will be going up on my wall. Very highly recommended! This was close to what I had in mind - different coding schemes to show individual relationships between aas. Taylor also has a chapter in the book "Nucleic Acid and Protein Sequence Analysis - A Practical Approach", Edited by M. J. Bishop and C. J. Rawlings, (IRL Press Oxford & Washington DC), 1987 that differs in topic, but includes some of the same information (thanks to Peter Floriani (florianp@cs.rpi.edu) for the pointer). Andre Lipinski (andre@xtliris.csu.McMaster.CA) and Calvin Harley (charley@mcmail.cis.mcmaster.ca) have "designed a set of rational graphic representations for presenting protein primary structure ... The implementation is via a Fortran77 program that produces a PostScript output, in colour of the sequence as a linear string of icons representing each different aa." They have also submitted the program to GCG for inclusion into their package. Andre writes: Our system is simply 2-dimensional giving information ranging from just the gross character of a sidechain (charged, hydrophilic and hydrophobic and sulphur containing) using four primary colours for each (red, blue, green and yellow) to form the body of a cube. To represent other aspects of the residue, a corner of the cube is coloured in the lessor character of the residue. We furthered this by changing the basic shape to give an indication of the size, and to a lessor degree, the shape of the side chain. Small residues have the bottom corner cut off, medium sized hav the cube shape, big residues have a cube plus a triangle added to the bottom, side-chains with some partial ring structure or long chain are a rectangle (resting on the short side) with one corner rounded off, really big residues like whole ring structures have a big appendage stuck to the bottom etc... This system has little degeneracy. The point was to show what it is like, not re-name it. A third method is a compromise for situations where abstractions will not suffice. It is simply a stylised representation of the structure of the side chain." They were good enough to send me color Postscript examples of their work. The examples are in 3 formats, small, medium, and large. While in color (using the SGI PS Viewer) even the smallest "characters" were easy to differentiate, in B+W, the small one is a bit ...small and the characteristics are hard to make out with the shading scheme they've implemented. The large size is useful, however, because they very nicely iconify the actual structure of the amino acid. I apologize for the somewhat base suggestion that they would be very useful as an Amino Acid 'font' to use in sequence alignments or in structural diagrams - much more useful than filled circles or stacks of text. I've asked them to put some examples up for anonymous FTP - write to them direct. Larry Hunter (hunter@nlm.nih.gov) responded with an entire paper (Postscript Format) which also hit very close to the mark. His thesis (correct me if I'm horribly off the mark) is that amino acids are usually represented by a very limited number of bits for machine learning and analysis. One reason for this is the the usual/easy way of representing characters in modern, general-purpose compilers (1 byte/character, referencing the character and conveying no other information about it). Certainly, if more information could be coded into the original representation of the amino acid, you would have to do less processing to derive relationships among the different aas or proteins. Larry proposes to use much longer (48 bit) bitstrings to represent amino acids, encoding in that bitstring the Atom/Orbital/Hydrogen (AOH) configuration of each. In this way, a substantial amount of the the bio-physico-chemical information about that amino acid is carried in its representation. While 48 bits is considerably longer than 8 (the standard length for a char), it is not unmanagably so, fitting nicely into 1.5 32-bit words, the standard data chunk of modern 32-bit processsors. He has carried out analyses using this representation in a neural network- based prediction of 'missing amino acids' and has found that it is always better than the simple naming representation and usually better than another method that uses 10-bit strings to represent aas (similar to the one described in Holley and Kaplus 1989). You can get the relevant files by anonymous ftp from the host lhc.nlm.nih.gov, in the directory /pub/amino-acid-rep. Gaston Gonnet (gonnet@inf.ethz.ch) contributed two ways of visualizing this kind of data: He writes: "We have been looking at representation of amino acids such that distance between them relates to likelihood of inter-mutation. Let me explain this in a bit more of detail. From a sufficiently large set of alignments (or from a Dayhoff matrix) you can compute the probability of amino acid i mutating into amino acid j for every i and j. This is known as a mutation matrix in the standard jargon. Now you make the analogy that distance between amino acids is inversely proportional to the probability of mutation. I.e. double the distance means half likely to mutate into each other. Hence, "close" amino acids will likely mutate into each other, "distant" amino acids are unlikely to mutate into each other. Close amino acids must have similar properties for protein function. To represent this information we have two alternatives. The first is to represent them as an unrooted tree. The amino acids are at the leaves and the distance between amino acids is measured by the length of all the branches that link the two together. This is very much like phylogenetic tree construction, except that it is done for similarities, not for common ancestry. The second method is to use euclidean distances and represent the 20 points in space. Two dimension placements give a rather primitive approximation, but is much easier to see than 3D (not to mention 4D, 5D, etc.). In both cases, for the unrooted tree and for the 2D placement, the constructions are approximations. It is generally impossible to find a tree or points in 2D which satisfy all 20*(20-1)/2=190 distance constraints. This message includes the postscript for the tree and for the 2D placement. This can be displayed in most bitmapped terminals and on postscript printers. The postscript files are separated by dashed lines. Enjoy it! Gaston H. Gonnet, Informatik, ETH Zurich." <<< In the interest of saving bandwidth, the PS files are not included here <<< but can be obtained from our anonymous FTP server (salk-sc2.sdsc.edu) in the <<< top directory as GONNET.PS (contains both files). He also responded to my mention of representing the relationships in multiple dimensions with a note to the effect that his group has already tried something along these lines and that (happily), _most_ of the information coded in such a 20D analysis can also be encoded in a 3D analysis. I look forward to reading the paper. Thanks to all who responded! If you have any advice or further comments, I'd love to hear them. Standard disclaimers apply. Cheers and Happy Holidays or So long and thanks for the fish, Harry (If you can't do it right, do it now) Mangalam Harry Mangalam Vox:(619) 453-4100, x250 Dept of Biocomputing Fax:(619) 552-1546 The Salk Institute 1' mangalam@salk-sc2.sdsc.edu 10010 N Torrey Pines Rd 2' hjm@salk-sgi.sdsc.edu La Jolla CA 92037 3' mangalam@salk.bitnet From owner-proteins@net.bio.net Wed Dec 16 22:00:00 1992 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Announcement of PIR Service Interruption Message-ID: <01GSF53X1DUA94E55H@NBRF.Georgetown.Edu> Date: 17 Dec 92 15:12:54 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 Announcement of Temporary Interruption of Access to The Protein Identification Resource The National Biomedical Research Foundation will be attempting to repair a hardware problem on Monday 21 December. From 10:00 EST Monday 21 December through about 12:00 EST Tuesday 22 December it will not be possible for users to access either the Protein Identification Resource Network Server or the On-line System. We regret any inconvenience this temporary loss of service will cause. ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Information Resource National Biomedical Research Foundation Washington, DC 20007 POSTMAST@GUNBRF.BITNET POSTMASTER@NBRF.GEORGETOWN.EDU From owner-proteins@net.bio.net Wed Dec 16 22:00:00 1992 Path: biosci!uwm.edu!spool.mu.edu!agate!stanford.edu!rutgers!mbcl!friedman From: friedman@mbcl.rutgers.edu Newsgroups: bionet.molbio.proteins Subject: Transcription factor with 2 activation sites??? Message-ID: <2093.2b2e61e2@mbcl.rutgers.edu> Date: 16 Dec 92 02:53:22 GMT Lines: 9 I am wondering if anyone has heard of a transcription factor which has two activation sites. I am trying to find out if a factor which binds to an enhancer sequence, has the ability to stimulate expression from two promoters, simultaneously. I think that this would require that the factor would have to have two activation sites. If you any info, please e-mail me . Thanks Rich Friedman@mbcl.rutgers.edu From owner-proteins@net.bio.net Wed Dec 16 22:00:00 1992 Path: biosci!bcm!tamsun.tamu.edu!cs.utexas.edu!sdd.hp.com!caen!uvaarpa!murdoch!cyclops.micr.Virginia.EDU!wrp From: wrp@cyclops.micr.Virginia.EDU (Bill Pearson) Newsgroups: bionet.molbio.proteins Subject: Jones, Thorton & Taylor Mutation Data Matrices Message-ID: <1992Dec18.025007.25990@murdoch.acc.Virginia.EDU> Date: 18 Dec 92 02:50:07 GMT Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia Lines: 11 Originator: wrp@cyclops.micr.Virginia.EDU I recall getting some datafiles and programs last May/June that allowed one to calculate new mutation data matrices based on the data accumulated by Jones et. al CABIOS (1992) 8:275. Unfortunately I cannot find the programs/data now and my mail to jones@bsm.bioc.ucl.ac.uk is rejected. I would greatly appreciate receiving a copy of those programs and datafiles. Bill Pearson From owner-proteins@net.bio.net Thu Dec 17 22:00:00 1992 Path: biosci!agate!spool.mu.edu!uunet!pipex!warwick!uknet!bcc.ac.uk!bsmsol1!jones From: jones@bsmsol1.ucl.ac.uk (David Jones) Newsgroups: bionet.molbio.proteins Subject: Re: Amino Acid Relationships (long) Message-ID: <1992Dec17.212646.28220@bas-a.bcc.ac.uk> Date: 17 Dec 92 21:26:46 GMT References: <9212162113.AA25053@salk-sgi.sdsc.edu> Sender: news@ucl.ac.uk (Usenet News System) Distribution: bionet Organization: University College London Biochemistry Department Lines: 42 As a follow-up to Harry Mangalam's summary of methods for representing amino acid similarities, people might also be interested in the following two references (one in press, one in print): The first paper is something of a sequel to Willie Taylor's original Venn diagram paper from 1986... Taylor, W.R., Jones, D.T. "Deriving an Amino Acid Distance Matrix." J. Theor. Biol. in press. (1993) ABSTRACT Various methods were investigated to convert an amino acid similarity matrix into a low-dimensional, metric distance matrix. Using projection techniques, no unique transformation was found and of the many inversion forms investigated, simple negation normalised by the diagonal elements produced a good fit to the original data. An inter-row distance also gave a comparable fit and when evaluated by weighted least-squares minimisation was found to be preferable. A rank-ordered form of the matrices was also derived by constraining neighbours to be equidistant in (3) space. This produced a network configuration not unlike that produced in a previous analysis of amino acid physico-chemical properties. The derived forms might find applications in sequence alignment, including pattern matching algorithms, and the construction of phylogenetic trees. The other reference is... Taylor, W.R. "A template based method of pattern matching in protein sequences." Prog. Biophys. Mol. Biol. 54:159-252 (1989) (published in 1991). This paper contains possibly the oldest reference in any molecular biology paper: Wan, "The I Ching", privately published (1142 BC). If you want to know what Gray codes, the I Ching, and the genetic code have to do with representing amino acid similarities, then this is the paper for you! --- David Jones Biomolecular Structure and Modelling Unit University College London From owner-proteins@net.bio.net Thu Dec 17 22:00:00 1992 Path: biosci!SALK-SC2.SDSC.EDU!mangalam From: mangalam@SALK-SC2.SDSC.EDU (Harry Mangalam) Newsgroups: bionet.molbio.proteins Subject: Re: Transcription factor with 2 activation sites??? Message-ID: <9212181813.AA27592@salk-sgi.sdsc.edu> Date: 18 Dec 92 18:13:20 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 36 Rich Friedman writes: >I am wondering if anyone has heard of a transcription factor which has two >activation sites. I am trying to find out if a factor which binds to an >enhancer sequence, has the ability to stimulate expression from two promoters, >simultaneously. I think that this would require that the factor would have to >have two activation sites. If you any info, please e-mail me . There are some transcription factors (TFs) that have multiple DNA binding domains - Mike Levine's lab characterized one (the name escapes me at the moment but I could look it up) that had both a "paired" box and a homeobox (homoeobox for the Brits) and both could bind to completely different (although in their original work, overlapping) sites. Recently, TFs have been cloned which have large numbers of Zn fingers (>15), many of which seem to be capable of binding DNA, and also recently someone cloned a monster that had multiple homeoboxes AND multiple Zn fingers. If your question is whether a TF with only one DNA binding site can activate multiple genes, then the answer is also yes, with examples too numerous to cover. A favorite example is the anterior pituitary-specific Pit1 (aka (if inaccurately) as GHF1) which can activate transcription from both the Prolactin promoter (and in fact is absolutely required for PRL expression), Growth Hormone promoter (less tightly regulated than PRL), and TSH gene, as well as its own promoter (all anterior pituitary-specific genes). Hope this is of some help Cheers, Harry Harry Mangalam Vox:(619) 453-4100, x250 Dept of Biocomputing Fax:(619) 552-1546 The Salk Institute 1' mangalam@salk-sc2.sdsc.edu 10010 N Torrey Pines Rd 2' hjm@salk-sgi.sdsc.edu La Jolla CA 92037 3' mangalam@salk.bitnet From owner-proteins@net.bio.net Thu Dec 17 22:00:00 1992 Path: biosci!uwm.edu!rpi!zaphod.mps.ohio-state.edu!saimiri.primate.wisc.edu!caen!spool.mu.edu!agate!doc.ic.ac.uk!uknet!bcc.ac.uk!bsm.bioc.ucl.ac.uk!jones From: jones@bsm.bioc.ucl.ac.uk (David Jones) Newsgroups: bionet.molbio.proteins Subject: Re: Jones, Thorton & Taylor Mutation Data Matrices Message-ID: <1992Dec19.004154.4577@bas-a.bcc.ac.uk> Date: 19 Dec 92 00:41:54 GMT References: <1992Dec18.025007.25990@murdoch.acc.Virginia.EDU> Sender: news@ucl.ac.uk (Usenet News System) Organization: University College London Biochemistry Dept. Lines: 15 My apologies to the people who have been trying to contact me via e-mail today. We've been trying out a new e-mail setup, and by some freak combination of events my e-mail aliases got messed up. I thought my mailbox was unusually quiet today... Just to confirm - the address jones@bsm.bioc.ucl.ac.uk is my correct (and now fully functional) e-mail address. David Jones Dept. of Biochemistry and Molecular Biology University College Gower Street London WC1E 6BT Tel. 071 387 7050 x3879 From owner-proteins@net.bio.net Fri Dec 18 22:00:00 1992 Path: biosci!agate!spool.mu.edu!caen!kuhub.cc.ukans.edu!husc-news.harvard.edu!husc10!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.molbio.proteins Subject: Re: Transcription factor with 2 activation sites??? (fwd) Message-ID: Date: 19 Dec 92 17:06:47 GMT References: <1992Dec19.131543.3183@gserv1.dl.ac.uk> Distribution: bionet Lines: 30 Nntp-Posting-Host: husc10.harvard.edu ghj@mrc-lmb.cam.ac.uk (Jacobs "G.") writes: >Just to add to the confusion, at least some of the DNA proteins with >more than one DNA binding domain can select between them via alt. >splicing. This could appear as activating at two different sites in >some assays I guess (I'm not an experimentalist, but it does seem an >obvious point...). >I could give you some examples later (I'm not at my lab. at the >moment). The Kafatos lab published a pair of papers on this in a recent Science (about 1 month ago?) >A point for myself is to distinguish between whether the protein binds >the two promoters *AT THE SAME TIME* or whether it is able to bind >the two promoters, but independently. Two very different things! >Grant Jacobs >MRC Laboratory of Molecular Biology >Hillls Road >Cambridge CB3 9EU >ENGLAND. Keith Robison Harvard University Department of Cellular & Developmental Biology Department of Genetics / HHMI robison@biosun.harvard.edu From owner-proteins@net.bio.net Fri Dec 18 22:00:00 1992 Path: biosci!uwm.edu!cs.utexas.edu!uunet!pipex!warwick!uknet!daresbury!news From: ghj@mrc-lmb.cam.ac.uk (Jacobs "G.") Newsgroups: bionet.molbio.proteins Subject: Re: Transcription factor with 2 activation sites??? (fwd) Message-ID: <1992Dec19.131543.3183@gserv1.dl.ac.uk> Date: 19 Dec 92 18:17:16 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 66 Original-To: proteins@uk.ac.daresbury Forwarded message: >From @dlgm.dl.ac.uk:bionet-news@dl.ac.uk Sat Dec 19 10:48:07 1992 >Date: Sat, 19 Dec 92 10:26:04 UT >Message-Id: <921219102604.MIN-LFBAa26371.bionet-news@uk.ac.daresbury> >From: mangalam@SALK-SC2.SDSC.EDU (Harry Mangalam) >Reply-To: mangalam@SALK-SC2.SDSC.EDU (Harry Mangalam) >Sender: "bionet.molbio.proteins mail newsgroup" >To: "bionet.molbio.proteins mail newsgroup" >Subject: Re: Transcription factor with 2 activation sites??? >X-Article-Number: bionet.molbio.proteins Msg # 139 >Comments: List problems/queries to >Comments: To mail both the group and netnews send to (proteins@daresbury.ac.uk) > >Rich Friedman writes: > >>I am wondering if anyone has heard of a transcription factor which has two >>activation sites. I am trying to find out if a factor which binds to an >>enhancer sequence, has the ability to stimulate expression from two promoters, >>simultaneously. I think that this would require that the factor would have to >>have two activation sites. If you any info, please e-mail me . > > There are some transcription factors (TFs) that have multiple DNA >binding domains - Mike Levine's lab characterized one (the name escapes me >at the moment but I could look it up) that had both a "paired" box and a >homeobox (homoeobox for the Brits) and both could bind to completely >different (although in their original work, overlapping) sites. Recently, >TFs have been cloned which have large numbers of Zn fingers (>15), many of >which seem to be capable of binding DNA, and also recently someone cloned a >monster that had multiple homeoboxes AND multiple Zn fingers. > If your question is whether a TF with only one DNA binding site can >activate multiple genes, then the answer is also yes, with examples too >numerous to cover. A favorite example is the anterior pituitary-specific >Pit1 (aka (if inaccurately) as GHF1) which can activate transcription from >both the Prolactin promoter (and in fact is absolutely required for PRL >expression), Growth Hormone promoter (less tightly regulated than PRL), and >TSH gene, as well as its own promoter (all anterior pituitary-specific >genes). > >Hope this is of some help >Cheers, >Harry > >Harry Mangalam Vox:(619) 453-4100, x250 >Dept of Biocomputing Fax:(619) 552-1546 >The Salk Institute 1' mangalam@salk-sc2.sdsc.edu >10010 N Torrey Pines Rd 2' hjm@salk-sgi.sdsc.edu >La Jolla CA 92037 3' mangalam@salk.bitnet > > > Just to add to the confusion, at least some of the DNA proteins with more than one DNA binding domain can select between them via alt. splicing. This could appear as activating at two different sites in some assays I guess (I'm not an experimentalist, but it does seem an obvious point...). I could give you some examples later (I'm not at my lab. at the moment). A point for myself is to distinguish between whether the protein binds the two promoters *AT THE SAME TIME* or whether it is able to bind the two promoters, but independently. Two very different things! Grant Jacobs MRC Laboratory of Molecular Biology Hillls Road Cambridge CB3 9EU ENGLAND. From owner-proteins@net.bio.net Mon Dec 21 22:00:00 1992 Path: biosci!agate!spool.mu.edu!uunet!timbuk.cray.com!walter.cray.com!snoid!mwd From: mwd@cray.com (Mark Dalton) Newsgroups: bionet.molbio.proteins Subject: Re: Signal predictions/scanning Summary: signal scanning Message-ID: <1992Dec22.134803.1531@walter.cray.com> Date: 22 Dec 92 19:48:03 GMT Followup-To: mwd@cray.com Organization: Cray Research, Inc. Lines: 51 Originator: mwd@snoid Nntp-Posting-Host: snoid.cray.com There are a few programs: -RegSearch - Searches for regulatory sites. -SigSeq - Searches for DNA signal motifs. -SignalScan - searches for signal motifs. -GM - searches for ORF's, regulation sites, and binding sites. 1. Signal Scan Analysis of DNA sequences for known eukaryotic signals LANL.GOV SignalScan - searches for signal sequences(Transcription factor DB, TFD) Signal scan is a program developed by Dan S. Prestridge, to facilitate the analysis of DNA sequences for known eukaryotic signals. This program is free. You may copy and distribute this program as freely as you wish, but you may not charge for its distribution. This program is copyrighted by Los Alamos National Laboratory and the University of California. The source code is written in the `C' language and is fairly easy to port over to other hardware and operating systems. The source code will be made available upon request. The author welcomes comments and suggestions, on the program or additions to the database. Please contact: Dan S. Prestridge Los Alamos National Laboratory Group T-10, MS K710 Los Alamos, NM 87545 E-mail: DXP%LIFE@LANL.GOV 2. SigSeq DNA signal sequence searches - ftp.bio.indiana.edu (129.79.1.101) 3.RegSearch Search for DNA regulatory sites I think this is also at- ftp.bio.indiana.edu (129.79.1.101) 4. GM (Gene Modeler) searches for ORF's, regulation sites, and binding sites haywire.nmsu.edu If you need any software feel free to contact me. Or if you have software I will try to build a complete list of what is available and what platforms it runs on. Thanks! Mark -- Mark Dalton Cray Research, Inc. Eagan, MN 55121 Internet: mwd@cray.com From owner-proteins@net.bio.net Thu Dec 24 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!news.acns.nwu.edu!uicvm.uic.edu!u59918 From: U59918@uicvm.uic.edu (Dong Li 312-996-0509) Newsgroups: bionet.molbio.proteins,bionet.software Subject: How to display 3D structure of PDB files with a PC? Message-ID: <92360.094143U59918@uicvm.uic.edu> Date: 25 Dec 92 15:41:43 GMT Organization: University of Illinois at Chicago Lines: 21 Xref: biosci bionet.molbio.proteins:474 bionet.software:3838 Dear Netters, I am trying to do the tertiary modeling now. I will be very grateful if you tell me how I can get a program to display with an IBM PC the tertiary or stereo structures of the proteins, based on the data files from Brookhaven Protein Database. Any help will be appreciated very much. By the way, thanks a lot to those who helped me previously. Due to the uncertain network problem, I failed to reply and say THANK YOU to some of them. Dong Li ************************************************************************* With malice toward none, with charity for all.......... Abraham Lincoln ------------------------------------------------------------------------- Dong Li Telephone: (312) 996-0509 Fax: (312) 413-2435 Internet: u53077@uicvm.uic.edu Bitnet: u53077@uicvm.bitnet Dept. Biological Sciences, Univ. Illinois at Chicago, Chicago, IL 60680 ************************************************************************* From owner-proteins@net.bio.net Mon Dec 28 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!usc!howland.reston.ans.net!paladin.american.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.proteins,bionet.software Subject: Re: How to display 3D structure of PDB files with a PC? Message-ID: <1992Dec29.170548.9873@welchgate.welch.jhu.edu> Date: 29 Dec 92 17:05:48 GMT References: <92360.094143U59918@uicvm.uic.edu> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 155 Xref: biosci bionet.molbio.proteins:475 bionet.software:3840 In article <92360.094143U59918@uicvm.uic.edu> Dong Li 312-996-0509 writes: >Dear Netters, > >I am trying to do the tertiary modeling now. I will be very grateful >if you tell me how I can get a program to display with an IBM PC >the tertiary or stereo structures of the proteins, based on the >data files from Brookhaven Protein Database. > >Any help will be appreciated very much. > >By the way, thanks a lot to those who helped me previously. >Due to the uncertain network problem, I failed to reply and say THANK YOU >to some of them. > >Dong Li ***************************************************************************** There was a discussion about this last summer as well as a followup earlier this month - there are pros and cons to using a PC for this type of work - much depends on what you want to do (but that's another discussion :-). Eric Hugo of Wash U. St. Louis posted the follwoing summary about the responses to his (similar) question. Regards, Dan Jacobson danj@welchgate.welch.jhu.edu ================================================================================ Of the answers I received one set of programs was mentioned that is available by anonymous ftp. These are shareware programs written at the University of Illinois and distributed by Dr. A.R Croft. These programs (pdViewer and PSAAM) are written in Visual Basic and run under Windows 3.x. I've just downloaded them and am in the process of evaluating them. The two programs can be obtained from nemo.life.uiuc.edu (128.174.183.6) in the pub/pdvwin and the pub/psaam subdirectories by anonymous ftp. Thanks to all of the individuals that responded to my query, the information was greatly appreciated. Eric ;-) SUMMARY INFORMATION: Tom Branham writes: I do know of a commercial program called HyperChem from Autodesk for which the educational price is $600, but they do have a full free to researchers program (if you keep them updated on your work, etc.) The program is not only a visual interface, but performs molecular orbital calculations and molecular dynamics. I have been very tempted to take them up on the research program, but the one thing worrying me is that it comes with a hardware key and I have serial ports that are not well behaved. If anyone else comes up with any other sugestions I would appreciate hearing about them, as I am running Quanta at the lab, on our SGI's, and then I am working with my own programs, lotus123 and Mathcad at home on the pdb files, but can not view them at home, a minor irritation. I also purchase the programs on my own rather than with lab moneys. I like to feel that I do not "live off " the lab grants, perhaps a sense of hubris I REally can not afford this month :) ........Tom Branham P. S. Dr. Pochapsky brought back the PDB and Atlas of sequences from the same meeting. Wasn't that a Nice suprise.....? Watson Ko writes: Alchemy III will do the job you want, but it will be very slow if you try to rotate(or whatever) since the program has to redraw the whole molecule. What I did was just showing the active site of the specific enzyme(or protein) and manipulated the molecule. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Watson Ko v999r36x@ubvms.cc.buffalo.edu Space, the final ... parking place! =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Jim Cassatt writes: I have been using a shareware version of PCMODEL. Check previous messages regarding availability. Included are two sample files for chymotrypsin and B-DNA obtained from the PDB. They can be viewed quite effectively with a 486, less so with a 386SX and poorly with an 8088. What I have not been able to find out is whether a program to convert PDB format to PCMODEL format is available. The main difficulty is generating a connect table. There are also two versions of PCMODET, one a shareware version and the other distributed by Gilbert at Indiana. His version does not have a conversion program. I awaiting a response from the author of the shareware program. Jim Cassatt Dr. Ferenc Czegledy writes: There are several ways that I know of to visualize PDB files in the MS-DOS environment: >>>1. Using pdViewer which one can obtained by anonymous ftp from >>>nemo.life.uiuc.edu >>>The package must be transferred using the binary protocol and runs >>>under Windows 3.1/3.0. 2. Using a package called Alchemy III (for Windows) which is available from Tripos Assoc. Inc. ,St. Louis, MO. Phone: 314-647-1099. 3. Using Chem-X from Chemical Design Inc., 200 Route 17 South, Suite 120, Mahwah, NJ 07430. phone: 201-529-3323. I have only seen the brochure for this package but it looks very impressive. The only problem is that it is very expensive: ~ $ 2,500.00/year. The software will self-destruct after 1 year but if you pay for an additional year the software is upgraded for you. Anyway, good luck and tell me if you hear of any additional approaches to visualization and modeling on the PC. -- Ferenc Czegledy Dept. Of Cardiology Columbia University 630 W 168th Street New York, NY 10032 email: ferenc@cucrd0.med.columbia.edu Rhee Hwan-Seok writes concerning the program MOBY The following is the snail-mail address of MOBY manufacturer. In my address file they have no e-mail address known. ---------------------------- Springer-Verlag Heidelberger Platz 3 W-1000 Berlin 33 F.R.G ( Germany ) Telex : 461723 Telefax : (06221)413982 ---------------------------- They will send you a demo disk FREE of charge. And the disk could be 3" or 5" on your request. e-mail : hyunerho@krsnucc1.BITNET -- Eric R. Hugo, Postdoctoral Research Associate |eric@bcserv.wustl.edu Dept. of Biochemistry and Molecular Biophysics| Washington University School of Medicine | Box 8231, St. Louis, MO 63110_________________| (314) 362-3342 From owner-proteins@net.bio.net Tue Dec 29 22:00:00 1992 Path: biosci!agate!usenet.ins.cwru.edu!gatech!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.proteins Subject: Re: Enzyme Commission Classifications On-Line? Message-ID: <1992Dec30.174916.4403@welchgate.welch.jhu.edu> Date: 30 Dec 92 17:49:16 GMT References: <1992Dec30.091242.18896@husc3.harvard.edu> <1992Dec30.161914.26607@welchgate.welch.jhu.edu> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 27 In article <1992Dec30.161914.26607@welchgate.welch.jhu.edu> danj@welchgate.welch.jhu.edu (Dan Jacobson) writes: >In article <1992Dec30.091242.18896@husc3.harvard.edu> robison1@husc10.harvard.edu (Keith Robison) writes: >>Does anyone out there know where I can find the Enzyme Commission >>classifications on-line (gopher would be great) or FTPable? >> >> >There is a Wais source with which you can search the EC-enzyme database, >and of course you can use the wais source through gopher. (Shameless plug: >you can find a link to it in the gopher hole at merlot.welch.jhu.edu in the > > --> 4. Genbank, PIR, Swiss_PROT and other Database Searches/ > >directory. :-) Unfortunately the waisserver which runs the searches seems to >be down at the moment - I've contacted the maintainer and hope it will be back >online soon, if not I may serve it here. > >(etc....) Not often I get to reply to one of my own messages :-). The waisserver which serves the EC-Enzyme database is back up. Thanks and kudos go to Thon de Boer for the fast response and quick action. Happy hunting, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-proteins@net.bio.net Tue Dec 29 22:00:00 1992 Path: biosci!uwm.edu!rpi!gatech!usenet.ins.cwru.edu!agate!spool.mu.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.proteins Subject: Re: Enzyme Commission Classifications On-Line? Message-ID: <1992Dec30.161914.26607@welchgate.welch.jhu.edu> Date: 30 Dec 92 16:19:14 GMT References: <1992Dec30.091242.18896@husc3.harvard.edu> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 36 In article <1992Dec30.091242.18896@husc3.harvard.edu> robison1@husc10.harvard.edu (Keith Robison) writes: >Does anyone out there know where I can find the Enzyme Commission >classifications on-line (gopher would be great) or FTPable? > > There is a Wais source with which you can search the EC-enzyme database, and of course you can use the wais source through gopher. (Shameless plug: you can find a link to it in the gopher hole at merlot.welch.jhu.edu in the --> 4. Genbank, PIR, Swiss_PROT and other Database Searches/ directory. :-) Unfortunately the waisserver which runs the searches seems to be down at the moment - I've contacted the maintainer and hope it will be back online soon, if not I may serve it here. If you'd like to ftp the whole database you can get it from (among other places) ncbi.nlm.nih.gov in the repository/enzyme directory, or (shameless plug :-) go to the gopher hole at (among other places) merlot.welch.jhu.edu and go into the --> 2. FTP Sites For Biology/ directory where there is a link into the ncbi site - ( 16. NCBI Repository FTP Archive /) in which you'll find the enzyme directory and the EC-enzyme database which you can retrieve - it will take a little while as the database is an 800K file - some gopher clients handle big files better than others. Best of luck and Happy New Year, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-proteins@net.bio.net Tue Dec 29 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!moe.ksu.ksu.edu!kuhub.cc.ukans.edu!husc-news.harvard.edu!husc10.harvard.edu!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.molbio.proteins Subject: Enzyme Commission Classifications On-Line? Message-ID: <1992Dec30.091242.18896@husc3.harvard.edu> Date: 30 Dec 92 14:12:42 GMT Organization: Harvard University Science Center Lines: 13 Nntp-Posting-Host: husc10.harvard.edu Does anyone out there know where I can find the Enzyme Commission classifications on-line (gopher would be great) or FTPable? Thanks. Keith Robison Harvard University Department of Cellular & Developmental Biology Department of Genetics / HHMI robison@biosun.harvard.edu From owner-proteins@net.bio.net Tue Dec 29 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!usc!sdd.hp.com!think.com!hsdndev!nmr-z!OPAL.MGH.HARVARD.EDU!CHERRY From: cherry@OPAL.MGH.HARVARD.EDU Newsgroups: bionet.molbio.proteins Subject: Re: Enzyme Commission Classifications On-Line? Message-ID: <1992Dec30.233116.19043@nmr-z.mgh.harvard.edu> Date: 30 Dec 92 23:31:16 GMT References: <1992Dec30.091242.18896@husc3.harvard.edu>,<1992Dec30.161914.26607@welchgate.welch.jhu.edu> Sender: usenet@nmr-z.mgh.harvard.edu (User for USENET news postings) Reply-To: cherry@OPAL.MGH.HARVARD.EDU Organization: Molecular Biology - Mass Gen Hospital Lines: 49 Nntp-Posting-Host: opal.mgh.harvard.edu Here is a description of Amos Bairoch's ENZYME database from the ENZYME User's Manual. Amos Bairoch Medical Biochemistry Department Centre Medical Universitaire 1211 Geneva 4 Switzerland Telephone: (+41 22) 361 84 92 Electronic mail address: BAIROCH@CMU.UNIGE.CH or BAIROCH@CGECMU51.BITNET 1.1) Definition of the scope of the data bank The 'ENZYME' data bank contains the following data for each type of characterized enzyme for which an EC number has been provided: - EC number. - Recommended name. - Alternative names (if any). - Catalytic activity. - Cofactors (if any). - Pointers to the SWISS-PROT entrie(s) that correspond to the enzyme (if any). - Pointers to disease(s) associated with a deficiency of the enzyme (if any). We believe that the ENZYME data bank will be useful to anybody working with enzymes and will allow programs to be developed that can help with the creation of new metabolic pathways. 1.2) Sources of the data The main source for the data in the ENZYME data bank comes from recommendations of the Nomenclature Committee of the International Union of Biochemistry (NC-IUB) [1,2,3,4]. A minor part of the data has been extracted from the literature. [1] Enzyme Nomenclature, NC-IUB, Academic Press, New-York, (1984). [2] Supplement 1: corrections and additions. Eur. J. Biochem. 157:1-26(1986). [3] Supplement 2: corrections and additions. Eur. J. Biochem. 179:489-533(1989). [4] Supplement 3: corrections and additions. Eur. J. Biochem. 187:263-281(1990). From owner-proteins@net.bio.net Wed Dec 30 22:00:00 1992 Path: biosci!daresbury!bioftp.unibas.ch!biox!rdoelz From: rdoelz@comp.bioz.unibas.ch (Reinhard Doelz [remote]) Newsgroups: bionet.molbio.proteins Subject: Re: Enzyme Commission Classifications On-Line? Message-ID: Date: 31 Dec 92 12:05:44 GMT References: <1992Dec30.091242.18896@husc3.harvard.edu> Organization: EMBnet Switzerland [Basel] Lines: 28 robison1@husc10.harvard.edu (Keith Robison) writes: >Does anyone out there know where I can find the Enzyme Commission >classifications on-line (gopher would be great) or FTPable? on the bioftp GOPHER server the ENZYME database is indexed and available for searching via gopher (port 70 on bioftp.unibas.ch). bioftp.unibas.ch gets also updated by Dr. Bairoch, to whom I am very grateful, in the framework of the European Molecular Biology Network, Swiss node, in the directory archive_data/database by anonymous ftp. The same server [131.152.8.1 for those without name server] has the EMBL CD-ROM mounted and therefore the current EMBL Version of the ENZYME database on-line. The host biomed.uio.no provides telnet login under the username srs (as managed by R.Lopez, srs is copyright T.Etzold) where you can search several molbio databases including xref annotation. Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz |