From owner-proteins@net.bio.net Wed Sep 01 23:00:00 1993 Path: biosci!UIDAHO.EDU!kellogg From: kellogg@UIDAHO.EDU (Scott Kellogg) Newsgroups: bionet.molbio.proteins Subject: Protein Instrumentation Message-ID: Date: 2 Sep 93 02:46:55 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 9 We are considering adding a faculty member in protein structure/function and we wondering which instruments at what costs are required for such an individual. The initial instruments that came to mind were: 2D NMR, CD, FTIR, protein synthesizer, protein sequencer, x-ray crystallograph. Are there are others? What are the primary needs for protein characterization? Approximately how expensive are these instruments and matching computers? From owner-proteins@net.bio.net Wed Sep 01 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!rigel.bmc.uu.se!gerard From: gerard@rigel.bmc.uu.se (Gerard Kleijwegt) Newsgroups: bionet.molbio.proteins Subject: Re: computer models of troponin C and Calmodulin Message-ID: <2657dg$ha0@corax.udac.uu.se> Date: 2 Sep 93 16:36:00 GMT References: <2653uv$h4q@corax.udac.uu.se> Organization: Uppsala University Lines: 45 NNTP-Posting-Host: rigel.bmc.uu.se Joe, I got your e-mail but can't mail you: Comment: Bad address -- Comment: Nameserver error: Unknown host anyway: the information comes from an ascii file containing the most important header records of all current PDB files; all i did was vi, search & cut&paste into my posting. there are two of these files, together ~1.5 MB if you're interested, i put compressed copies on our ftp server: daisy.bmc.uu.se (130.228.37.22); login as user ftp, password your e-mail address, cd pub/various, binary, mget header* if you want more information about the PDB, send a mail to pdb@chm.chm.bnl.gov let me know when you've ftp-ed the files, so i can remove them again hope this helps hejda, --gerard -- ****************************************************************** Gerard J. Kleywegt _____ Department of Molecular Biology | | / \ Biomedical Centre / \ --- | | University of Uppsala | | | | | | Uppsala | | | | | | SWEDEN | | \ / --- --- |____| E-mail: gerard@xray.bmc.uu.se ****************************************************************** "He's probably pining for the fiords ..." ****************************************************************** The opinions in this mail/post are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ****************************************************************** From owner-proteins@net.bio.net Wed Sep 01 23:00:00 1993 Path: biosci!rutgers!cs.utexas.edu!uunet!pipex!zaphod.crihan.fr!univ-lyon1.fr!cri.ens-lyon.fr!ibcp.fr!deleage From: deleage@ibcp.fr (G.Delage) Newsgroups: bionet.molbio.proteins Subject: ANTHEPROT: A package for protein sequence analysis Message-ID: <264ud7$fbm@cri.ens-lyon.fr> Date: 2 Sep 93 14:02:15 GMT Organization: Institut de Biologie et Chimie des Proteines. CNRS-Lyon Lines: 120 NNTP-Posting-Host: ibcp.fr X-Newsreader: TIN [version 1.1 PL8] -- ------------------------------------------------------------------------ # # # ####### # # ####### ###### ###### ####### ####### # # ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # ####### ##### ###### ###### # # # ####### # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # ####### # # # ####### # ----------------------------------------------------------------------- by G.Deleage & C. Geourjon This is a general annoucement of the availability of ANTHEPROT to all academic researchers. ANTHEPROT (ANalyze THE PROTeins) is a package to make protein sequence analysis such as alignment, secondary structure predictions, sites & function detection, physico-chemical profiles, homology search and 3D display of protein structures. This program is now available either for IBM RISC 6000 workstations or IBM PC compatible microcomputers. The main feature of ANTHEPROT is that it is fully interactive within a graphical interface. No particular knowledge about computers is needed and any mole- cular biologist is able to use it. The main methods are: * Input, addition or modification of sequences (FASTA format). * Edition (graphic display of sequence, molecular weight,...). * Extraction of a sequence from databases (SWISSPROT). * Search for subsequences (with pattern matching approach). * Dot matrix plot (4 substitution matrix). * Secondary structure prediction (6 methods). * Profile analysis (Hydrophobicity, flexibility, solvant accessibility, membrane spanning regions, antigenicity,...). * Amphiphilicity of secondary structure. * Prediction of the cleavage site of signal peptide. * Helical wheel projection. * Protein digestion and RP-HPLC simulations. * Circular dichroism spectra analysis. * Search for pattern of biological sites and functions (PROSITE). * Matrix profile analysis of blocks (BLOCKS.DAT). * Multiple alignment methods. * Fasta graphical interface. IBM RISC 6000 version ===================== This version can be considered as a molecular graphic software that is very useful to those who want to play with molecular modelling of proteins. These graphic capabilities are combined with many powerful tools to analyze a protein sequence and structure. The ANTHEPROT package is made of more than 71 submenus which account for about 30 different methods of protein sequence analysis. The complete package represents: 50 000 lines of source code 500 subroutines 1 3000 000 octets of source code 2 6800 000 octets for the antheprot executable file Systems and materials --------------------- ANTHEPROT can run on all IBM Risc 6000 computer equipped with a 3 D graphic adapter (with or without Z buffer, 8 or 24 bits plane) with graPHIGS libraries installed (libgP.a). The perfect configuration : IBM Risc 6000 (any model of CPU from 220 to 580) with at least 32 Mo of RAM), valuators, LPFK, 3 D+ graphic adapter with 24 bits plane + Z buffer or GT4x and GTO graphic cards. About 160 Mo of disk place is needed since the SWISSPROT and the NBRF/PIR protein sequence databases are also included. Distribution support : 150Mo streamer cartridge. References: C. Geourjon, G. Deleage and B. Roux ANTHEPROT : An interactive graphic software for analyzing protein structures from sequences. J. Mol. Graph., 1991, 9, 188-190 Geourjon C., Deleage G. Interactive and graphic coupling between multiple alignments, secondary structure predictions and motif/pattern scanning into proteins. Comput. Appl. Biosci. 9:87-91(1993). G. Deleage and C. Geourjon An interactive graphic program for calculating secondary structures content of proteins from circular dichroism spectrum. CABIOS, 1993, 9, 197-199 IBM PC compatible version ========================= The methods are essentailly the same than in the RISC 6000 except for the 3D display module. ANTHEPROT works onto all 80x86 with x>=2 processors. Math coprocessor is fully supported. The total disk space needed is about 5Mo. It is supplied onto 2 HD (1.44Mo) disks. An automatic installation menu is available by typing A:install The maximal graphic resolution supported is VGA (640x480). The program can be fully mouse driven (Microsoft compatible). Distribution support : 2 MS-DOS fomatted HD disks (1.44Mo) References: G. Deleage, FF Clerc and B Roux ANTHEPROT: IBM PC and Apple Macintosh versions. CABIOS, (1989) 5, 159-160 G. Deleage, FF Clerc, B Roux and DC Gautheron ANTHEPROT: A package for protein sequence analysis using a microcomputer. CABIOS, (1988) 5, 159-160 ===================================================================== # Institut de Biologie et Chimie des Proteines. UPR 412-CNRS # # ***** ***** **** ***** Dr Gilbert Deleage # # # # # # # # # 7, passage du Vercors # # # ***** # # # 69367 Lyon Cedex 07 # # # # # # #**** Tel: (33) 72-72-26-47 # # # # # # # # Fax: (33) 72-72-26-01 # # ***** ****** **** # deleage@ibcp.fr # ===================================================================== From owner-proteins@net.bio.net Wed Sep 01 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!spool.mu.edu!howland.reston.ans.net!noc.near.net!news.Brown.EDU!as.tsa.brown.edu!jel From: jel@as.tsa.brown.edu (Joe Lucas) Newsgroups: bionet.molbio.proteins Subject: computer models of troponin C and Calmodulin Message-ID: Date: 2 Sep 93 03:21:18 GMT Organization: Advanced Systems Lines: 3 NNTP-Posting-Host: 128.148.134.182 Does anyone know of any computer models of these proteins, and if so could you site some sources? -Joe From owner-proteins@net.bio.net Wed Sep 01 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!corax.udac.uu.se!rigel.bmc.uu.se!gerard From: gerard@rigel.bmc.uu.se (Gerard Kleijwegt) Newsgroups: bionet.molbio.proteins Subject: Re: computer models of troponin C and Calmodulin Message-ID: <2653uv$h4q@corax.udac.uu.se> Date: 2 Sep 93 15:37:03 GMT References: Organization: Uppsala University Lines: 164 NNTP-Posting-Host: rigel.bmc.uu.se In article , jel@as.tsa.brown.edu (Joe Lucas) writes: |> Does anyone know of any computer models of these proteins, and if so could |> you site some sources? |> -Joe Calmodulin in the FULL PDB release: ... FILE 1trc.pdb ... ID 1trc ... HEADER CALCIUM BINDING PROTEIN 18-JAN-90 1TRC REVDAT 1 15-OCT-91 1TRC 0 COMPND CALMODULIN (/TR=2=C$ FRAGMENT COMPRISING RESIDUES 78 - 148 COMPND 2 OF THE INTACT MOLECULE) SOURCE BULL (BOS $TAURUS) TESTES AUTHOR L.SJOLIN,L.A.SVENSSON,E.PRINCE,S.SUNDELL JRNL AUTH L.SJOLIN,L.A.SVENSSON,E.PRINCE,S.SUNDELL JRNL TITL PHASE IMPROVEMENT IN THE STRUCTURE INTERPRETATION JRNL TITL 2 OF FRAGMENT /TR=2=C$ FORM BULL TESTIS CALMODULIN JRNL TITL 3 USING COMBINED ENTROPY MAXIMIZATION AND SOLVENT JRNL TITL 4 FLATTENING JRNL REF ACTA CRYSTALLOGR.,SECT.B V. 46 209 1990 JRNL REFN ASTM ASBSDK DK ISSN 0108-7681 622 ... FILE 2cln.pdb ... ID 2cln ... HEADER CALCIUM BINDING PROTEIN 03-FEB-88 2CLN 2CLN 3 REVDAT 1 16-JUL-88 2CLN 0 2CLN 8 COMPND N==Z115== TRIMETHYLCALMODULIN COMPLEX WITH TRIFLUOPERAZINE 2CLN 4 COMPND 2 (MODEL) 2CLN 5 SOURCE BOVINE (BOS $TAURUS) BRAIN 2CLN 6 AUTHOR N.C.J.STRYNADKA,M.N.G.JAMES 2CLN 7 JRNL AUTH N.C.J.STRYNADKA,M.N.G.JAMES 2CLN 9 JRNL TITL TWO TRIFLUOPERAZINE-*BINDING SITES ON CALMODULIN 2CLN 10 JRNL TITL 2 PREDICTED FROM COMPARATIVE MOLECULAR MODELLING 2CLN 11 JRNL TITL 3 WITH TROPONIN-*C 2CLN 12 JRNL REF PROTEINS.STRUCT.,FUNCT., V. 3 1 1988 2CLN 13 JRNL REF 2 GENET. 2CLN 14 JRNL REFN ASTM PSFGEY US ISSN 0887-3585 867 2CLN 15 ... FILE 3cln.pdb ... ID 3cln ... HEADER CALCIUM BINDING PROTEIN 11-MAY-88 3CLN REVDAT 2 09-JAN-89 3CLNA 1 JRNL REVDAT 1 16-JUL-88 3CLN 0 COMPND CALMODULIN SOURCE RAT (RATTUS $RATTUS) TESTIS AUTHOR Y.S.BABU,C.E.BUGG,W.J.COOK REVDAT 2 09-JAN-89 3CLNA 1 JRNL JRNL AUTH Y.S.BABU,C.E.BUGG,W.J.COOK JRNL TITL STRUCTURE OF CALMODULIN REFINED AT 2.2 ANGSTROMS JRNL TITL 2 RESOLUTION JRNL REF J.MOL.BIOL. V. 204 191 1988 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 070 REMARK 6 CORRECTION. UPDATE JRNL REFERENCE TO REFLECT PUBLICATION. ... FILE 4cln.pdb ... ID 4cln ... HEADER CALCIUM BINDING PROTEIN 24-JUN-91 4CLN 4CLN 2 REVDAT 1 15-JUL-92 4CLN 0 4CLN 6 COMPND CALMODULIN 4CLN 3 SOURCE (DROSOPHILA $MELANOGASTER) EXPRESSED IN (ESCHERICHIA $COLI) 4CLN 4 AUTHOR D.A.TAYLOR,J.S.SACK,J.F.MAUNE,K.BECKINGHAM,F.A.QUIOCHO 4CLN 5 JRNL AUTH D.A.TAYLOR,J.S.SACK,J.F.MAUNE,K.BECKINGHAM, 4CLN 7 JRNL AUTH 2 F.A.QUIOCHO 4CLN 8 JRNL TITL STRUCTURE OF A RECOMBINANT CALMODULIN FROM 4CLN 9 JRNL TITL 2 DROSOPHILA $MELANOGASTER REFINED AT 2.2-*ANGSTROMS 4CLN 10 JRNL TITL 3 RESOLUTION 4CLN 11 JRNL REF J.BIOL.CHEM. V. 266 21375 1991 4CLN 12 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 071 4CLN 13 Calmodulin in the PDB PRE-release: ... FILE 1cll.pdb ... ID 1cll ... HEADER PRELIMINARY 29-SEP-92 P1CLL COMPND CALMODULIN (VETEBRATE) SOURCE RECOMBINANT PROTEIN USING VETEBRATE SEQUENCE AUTHOR R.CHATTOPADHYAYA,F.A.QUIOCHO ... FILE 1clm.pdb ... ID 1clm ... HEADER PRELIMINARY 23-JAN-93 P1CLM COMPND CALMODULIN FROM PARAMECIUM TETRAURELIA (WILD TYPE) SOURCE PARAMECIUM TETRAURELIA AUTHOR M.SUNDARALAINGAM ... FILE 2bbm.pdb ... ID 2bbm ... HEADER PRELIMINARY 16-JUL-92 P2BBM EXPDTA NMR COMPND CALCIUM-BOUND CALMODULIN COMPLEX WITH CALMODULIN BINDING COMPND 2 DOMAIN OF RABBIT SKELETAL MYOSIN LIGHT CHAIN KINASE COMPND 3 (MINIMIZED AVERAGE STRUCTURE PLUS 21 MODELS) SOURCE (DROSOPHILA $MELANOGASTER) AND SYNTHETIC PEPTIDE AUTHOR G.M.CLORE,A.BAX,M.IKURA,A.M.GRONENBORN Troponin in the FULL PDB release: ... FILE 1tnc.pdb ... ID 1tnc ... HEADER CONTRACTILE SYSTEM PROTEINS 15-JUL-80 1TNC 1TNC 3 REVDAT 2 30-SEP-83 1TNCA 1 REVDAT 1TNCA 1 REVDAT 1 09-AUG-80 1TNC 0 1TNCA 2 REMARK 6 CORRECTION. INSERT REVDAT RECORDS. 30-SEP-83. 1TNCA 4 COMPND TROPONIN - CALCIUM-BINDING COMPONENT 1TNC 4 SOURCE RABBIT (ORYCTOLAGUS CUNICULUS) 1TNC 5 AUTHOR R.H.KRETSINGER,C.D.BARRY 1TNC 6 JRNL AUTH R.H.KRETSINGER,C.D.BARRY 1TNC 7 JRNL TITL THE PREDICTED STRUCTURE OF THE CALCIUM-BINDING 1TNC 8 JRNL TITL 2 COMPONENT OF TROPONIN 1TNC 9 JRNL REF BIOCHIM.BIOPHYS.ACTA V. 405 40 1975 1TNC 10 JRNL REFN ASTM BBACAQ NE ISSN 0006-3002 113 1TNC 11 ... FILE 4tnc.pdb ... ID 4tnc ... HEADER CONTRACTILE SYSTEM PROTEIN 28-SEP-87 4TNC REVDAT 2 19-APR-89 4TNCA 1 JRNL REVDAT 1 16-JUL-88 4TNC 0 COMPND TROPONIN C SOURCE CHICKEN (GALLUS $GALLUS) SKELETAL MUSCLE REMARK 2 COLLECTED AT THE CORNELL HIGH ENERGY SYNCHROTRON SOURCE. AUTHOR M.SUNDARALINGAM REVDAT 2 19-APR-89 4TNCA 1 JRNL JRNL AUTH K.A.SATYSHUR,S.T.RAO,D.PYZALSKA,W.DRENDEL, JRNL AUTH 2 M.GREASER,M.SUNDARALINGAM JRNL TITL REFINED STRUCTURE OF CHICKEN SKELETAL MUSCLE JRNL TITL 2 TROPONIN C IN THE TWO-CALCIUM STATE AT 2-*ANGSTROMS JRNL TITL 3 RESOLUTION JRNL REF J.BIOL.CHEM. V. 263 1628 1988 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 071 ... FILE 5tnc.pdb ... ID 5tnc ... HEADER CONTRACTILE SYSTEM PROTEINS 27-MAY-88 5TNC REVDAT 2 09-JAN-89 5TNCA 1 JRNL SEQRES REVDAT 1 09-OCT-88 5TNC 0 COMPND TROPONIN-*C SOURCE TURKEY (MELEAGRIS $GALLOPAVO) SKELETAL MUSCLE AUTHOR O.HERZBERG,M.N.G.JAMES REVDAT 2 09-JAN-89 5TNCA 1 JRNL SEQRES JRNL AUTH O.HERZBERG,M.N.G.JAMES JRNL TITL REFINED CRYSTAL STRUCTURE OF TROPONIN C FROM TURKEY JRNL TITL 2 SKELETAL MUSCLE AT 2.0 ANGSTROMS RESOLUTION JRNL REF J.MOL.BIOL. V. 203 761 1988 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 070 Troponin in the PDB PRE release: ... FILE 1cta.pdb ... ID 1cta ... HEADER PRELIMINARY 12-NOV-92 P1CTA EXPDTA NMR COMPND CHICKEN SKELETAL TROPONIN C SITE III-SITEIII HOMODIMER COMPND 2 SCIII HOMODIMER N-ACETYL-(A101,Y112)-TROPONINC(93-126)- COMPND 3 AMIDE DIMER SOURCE SYNTHETIC PEPTIDE AUTHOR G.S.SHAW,B.D.SYKES --Gerard ****************************************************************** Gerard J. Kleywegt _____ Department of Molecular Biology | | / \ Biomedical Centre / \ --- | | University of Uppsala | | | | | | Uppsala | | | | | | SWEDEN | | \ / --- --- |____| E-mail: gerard@xray.bmc.uu.se ****************************************************************** "He's probably pining for the fiords ..." ****************************************************************** The opinions in this mail/post are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ****************************************************************** From owner-proteins@net.bio.net Thu Sep 02 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!ibmpcug!demon!visigoth.demon.co.uk!user From: pettsj@visigoth.demon.co.uk (James Petts) Newsgroups: bionet.molbio.proteins Subject: p56lck sh2 domain structure. Message-ID: Date: 2 Sep 93 00:33:19 GMT Sender: news@demon.co.uk (Usenet Administration) Followup-To: bionet.molbio.proteins Organization: No Affiliation Lines: 6 Nntp-Posting-Host: visigoth.demon.co.uk Does anybody know if the p56lck sh2 domain structure is available yet? -- -------- James Petts --------- ---- Beware of the Trund! ---- ------------------------------ From owner-proteins@net.bio.net Mon Sep 06 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!mcsun!sun4nl!star.cs.vu.nl!balaena!mac134.bio.vu.nl!user From: quido@bio.vu.nl (quido) Newsgroups: bionet.molbio.proteins Subject: HELP: beta-strand (sheet) prediction!! Message-ID: Date: 7 Sep 93 10:56:09 GMT Sender: news@bio.vu.nl Followup-To: bionet.molbio.proteins Organization: vu Lines: 15 Hello, I'm looking for a program which can predict beta-strands and/or beta-sheets from primary structures. Preferentially a program that has been used by auteurs before (reference would be nice) If you know how I can get such a program, please contact me as soon as possible. Thanks for the effort! -- Q. Valent, Free University of Amsterdam, Boelelaan 1087, 1081 HV, Amsterdam, The Netherlands. Fax: +3120-6429202, E-mail: quido@bio.vu.nl or valent@bio.vu.nl From owner-proteins@net.bio.net Tue Sep 07 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!spool.mu.edu!darwin.sura.net!news.gdb.org!dev.gdb.org!danj From: danj@dev.gdb.org (Dan Jacobson) Newsgroups: bionet.molbio.proteins Subject: Re: computer models of troponin C and Calmodulin Message-ID: <1993Sep8.215846.2300@news.gdb.org> Date: 8 Sep 93 21:58:46 GMT References: <2653uv$h4q@corax.udac.uu.se> <2657dg$ha0@corax.udac.uu.se> Sender: news@news.gdb.org Organization: Johns Hopkins University Genome Data Base (GDB) Lines: 29 Nntp-Posting-Host: dev.gdb.org In article <2657dg$ha0@corax.udac.uu.se> gerard@rigel.bmc.uu.se (Gerard Kleijwegt) writes: >Joe, I got your e-mail but can't mail you: > >Comment: Bad address -- >Comment: Nameserver error: Unknown host > >anyway: > > the information comes from an ascii file containing the most > important header records of all current PDB files; all i did > was vi, search & cut&paste into my posting. > there are two of these files, together ~1.5 MB > if you're interested, i put compressed copies on our ftp > server: daisy.bmc.uu.se (130.228.37.22); login as user > ftp, password your e-mail address, cd pub/various, > binary, mget header* > Perhaps a slightly easier solution for people with a network connection is to search (the headers) and retrieve the entire entries via gopher. If anyone has never heard of gopher write me a note and I'll send you some information to help get you started. Best of luck, Dan Jacobson danj@mail.gdb.org From owner-proteins@net.bio.net Wed Sep 08 23:00:00 1993 Path: biosci!ag.auburn.edu!Anthony.Johnson From: Anthony.Johnson@ag.auburn.edu (Anthony Johnson) Newsgroups: bionet.molbio.proteins Subject: soybean proteins Message-ID: <9309091912.AA27294@ag.auburn.edu> Date: 9 Sep 93 19:12:36 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 4 I am working with SOYBEANS and analyzing the induction of PR PROTEINS upon infection with C. sojina using SDS-PAGE and Western blot analysis. I am trying to find anyone out there who might have any experience in this area. Any input is welcome . Thanks Anthony Johnson (Auburn, AL) From owner-proteins@net.bio.net Wed Sep 08 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!mcsun!julienas!pasteur.fr!pasteur.fr!not-for-mail From: pmartino@pasteur.fr Newsgroups: bionet.molbio.proteins Subject: exported cytoplasmic proteins Message-ID: <26nloe$auk@mendel.sis.pasteur.fr> Date: 9 Sep 93 16:31:10 GMT Distribution: bionet Organization: Institut Pasteur, Paris, France Lines: 7 NNTP-Posting-Host: mendel.sis Hi Netters, I would like to know if somebody knows a report of successful exportation of a cytoplasmic protein. Thank you From owner-proteins@net.bio.net Thu Sep 09 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!gatech!hubcap!bounce-back From: hoffman@cs.unc.edu (Doug Hoffman) Newsgroups: bionet.molbio.proteins,sci.chem,sci.bio,comp.parallel Subject: specialized hardware for protein structure prediction Keywords: custom hardware protein structure molecular dynamics Message-ID: <1993Sep10.143016.16067@hubcap.clemson.edu> Date: 9 Sep 93 16:55:04 GMT Sender: fpst@hubcap.clemson.edu (Steve Stevenson) Organization: Department of Computer Science, UNC Chapel Hill Lines: 27 Approved: parallel@hubcap.clemson.edu Xref: biosci bionet.molbio.proteins:857 sci.chem:6831 sci.bio:4787 comp.parallel:3145 Nntp-Posting-Host: ravel.cs.unc.edu Follow-Up: comp.parallel I am in the process of writing a paper surveying the application of custom computational hardware to the problem of protein structure prediction. I am interested in any information regarding custom systems proposed, designed, or built that deal with protein folding, conformational energy calculations, secondary structure identification, molecular dynamics, etc. An example of the type of project that I'm interested in is the Delft Molecular Dynamics Processor, designed and constructed at the University of Technology at Delft, the Netherlands. I am not restricting my investigation to MD methods, information on projects pertaining to any facet of protein structure prediction is eagerly sought. If you know of or, better still, have been involved in such a project I would very much like to hear from you. If there are papers, tech reports, or other documents that can be e-mailed or ftp'ed I shall be extremely grateful. This survey is the first step towards a possible system building project at UNC-CH. The knowledge gained by any prior efforts will be highly valued by the researchers here. Regards, Doug ============================================================================= Doug L. Hoffman | University of North Carolina - Chapel Hill 3213 NC 62 East | hoffman@cs.unc.edu Liberty, NC 27298 | Work: (919) 962-1968, Home: (919) 565-4845 ============================================================================= From owner-proteins@net.bio.net Thu Sep 09 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!husc10.harvard.edu!beeson From: beeson@husc10.harvard.edu (Nicholas Beeson) Newsgroups: bionet.molbio.proteins Subject: Re: HELP: beta-strand (sheet) prediction!! Summary: structure prediction Message-ID: <26qkvr$sbs@scunix2.harvard.edu> Date: 10 Sep 93 19:36:27 GMT References: Organization: Harvard University Science Center Lines: 16 NNTP-Posting-Host: husc10.harvard.edu You want to get a copy of the procedings from the "First International Conference on Intelligent Systems for Molecular Biology." This was a refereed conference and the papers were published in the proceedings. I attended that conference and there were a DOZEN papers on secondary structure prediction programs. Some of them are amazingly effective. PROCEDINGS: First International Conference on Intelligent Sys- tems for Molecular Biology Editors: Lawerence Hunter, David Searls, & Jude Shavlik Publisher: AAAI Press, Menlo Park, California (1993) ISBN: 0-929280-47-4 -- Nick Beeson nick@heimdall.med.harvard.edu From owner-proteins@net.bio.net Thu Sep 09 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!noc.near.net!das-news.harvard.edu!husc-news.harvard.edu!husc.harvard.edu!husc10.harvard.edu!beeson From: beeson@husc10.harvard.edu (Nicholas Beeson) Newsgroups: bionet.molbio.proteins Subject: Proteins involved in DNA transcription Message-ID: <26r9gk$abm@scunix2.harvard.edu> Date: 11 Sep 93 01:26:44 GMT References: <9309110030.AA12296@net.bio.net> Distribution: bionet Organization: Harvard University Science Center Lines: 22 NNTP-Posting-Host: husc10.harvard.edu We are looking for collaboration opportunities with molecular biology groups that are involved in the study of proteins involved in the transcription of DNA. I am part of a structural biology group with extensive experience in solving the solution structure of proteins ( using NMR spectroscopy.) ( I am a postdoc in Gerhard Wagner's lab at the Harvard Medical School). A requirement for protein structure determination by NMR is that it is necessary to enrich the proteins with 15N and 13C. Therefore, a high level of expression in a suitable host (e.g. E. Coli ) is essential. If you are working with such a protein, and have the necessary expression system set up and if you are interested in collaboration with a lab that can determine the solution structure of such a protein, please contact me by e-mail at sekhar@heimdall.med.harvard.edu -- Sekhar Talluri sekhar@heimdall.med.harvard.edu From owner-proteins@net.bio.net Thu Sep 09 23:00:00 1993 Path: biosci!FDACFSAN.BITNET!FOF From: FOF@FDACFSAN.BITNET Newsgroups: bionet.molbio.proteins Subject: Export of cytoplasmic proteins. Message-ID: <9309110030.AA12296@net.bio.net> Date: 11 Sep 93 00:19:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 14 In response to request for info on export of cytoplasmic proteins, yes there is such a thing. Karl Kuchler, when he was in Jeremy Thorner's lab at Berkeley, sequeced the STE6 gene, which turned out to be a MDR homolog. In case you don't know, and there is no reason why you should, MDR is the multidrug resistance gene that, when massivley amplified, results in tumor cells that are capable of transporting cancer drugs out of the cytoplasm and are therefore resistant to the drugs. Back to the point. STE6 is involved in transporting the a-factor mating peptide out of the cytoplasm of yeast cells. Rachel Sterne when she was in the Thorner lab showed quite nicely that a-factor was cytoplasmic initially and can be exported *independently* of the SEC genes. SEC genes encode elements of the yeast secretory pathway and are it turns out often highly functionally and structurally similar to genes encoding proteins involved in mamalian secretion. For more info, do a search on Kuchler and Thorner or on Randy Shekman. From owner-proteins@net.bio.net Thu Sep 09 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!gatech!hubcap!bounce-back From: vanslyke@chem1.chem.dal.ca (VANSLYKE STEPHEN) Newsgroups: bionet.molbio.proteins,sci.chem,sci.bio,comp.parallel Subject: Re: specialized hardware for protein structure prediction Keywords: custom hardware protein structure molecular dynamics Message-ID: <1993Sep10.202227.14386@hubcap.clemson.edu> Date: 10 Sep 93 20:22:27 GMT Sender: fpst@hubcap.clemson.edu (Steve Stevenson) Organization: Dalhousie University, Halifax, Nova Scotia Lines: 11 Approved: parallel@hubcap.clemson.edu Xref: biosci bionet.molbio.proteins:859 sci.chem:6839 sci.bio:4794 comp.parallel:3155 Follow-Up: comp.parallel Doug, I have read some papers about the use of genetic algorithms in searching the conformation space of protein structure. These involve the work of Carlos Lucasius and Gerrit Kateman at the University of Nijmegen, the Netherlands. Although they do not mention any specialized hardware, this seems (to a naive chemist) to be a suitable problem for it. Let me know if this is of any use to you. Carlos is taking a postdoc position in our lab this fall, I imagine he would be interested in your work. Stephen Vanslyke Dalhousie University From owner-proteins@net.bio.net Sun Sep 12 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!europa.eng.gtefsd.com!news.ans.net!malgudi.oar.net!chemabs!ljc55 From: ljc55@cas.org Newsgroups: bionet.molbio.proteins Subject: PCR primers and hybridization probes Keywords: biosequence database PCR primer and hybridization probe Message-ID: <1993Sep13.174504.21635@cas.org> Date: 13 Sep 93 17:45:04 GMT References: <9309091912.AA27294@ag.auburn.edu> Sender: usenet@cas.org Reply-To: ljc55@cas.org Organization: Chemical Abstracts Service Lines: 28 For those of you interested in PCR primers and hybridization probes I would really appreciate your opinions about their inclusion in biosequence databases. Some of my specific concerns are as follows: 1. Do you feel primers and probes tend to clutter up a nucleic acid database and cause unnecessary retrievals when searching for sequences of much longer length? 2. Because primers and probes are usually designed from known sequence information often already in the database, is it still justifiable to include them as additional entries? 3. What applications of primers and probes should justify their inclusion in a biosequence database, e.g. clinical diagnosis, taxonomy, evolution, gene mapping, or methods? 4. If you were to search for primers and probes in a biosequence database what would be most efficient for you? Would some type of descriptive information be helpful, e.g. their application or their origin? Thank you very much for any thoughts you might have on this subject. Please post your response to ljc55@cas.org From owner-proteins@net.bio.net Sun Sep 12 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!europa.eng.gtefsd.com!howland.reston.ans.net!xlink.net!rz.uni-karlsruhe.de!news.uni-stuttgart.de!news.belwue.de!news.uni-freiburg.de!sun1.ruf.uni-freiburg.de!dikay From: dikay@sun1.ruf.uni-freiburg.de (Kay Diederichs) Newsgroups: bionet.molbio.proteins Subject: Re: HELP: beta-strand (sheet) prediction!! Message-ID: <27248n$3g4@sun8.ruf.uni-freiburg.de> Date: 13 Sep 93 15:40:07 GMT References: <26qkvr$sbs@scunix2.harvard.edu> Organization: Rechenzentrum der Universitaet Freiburg, Germany Lines: 13 NNTP-Posting-Host: sun1.ruf.uni-freiburg.de Hi everyone, one doesn't have to write one's own algorithm from a paper or get a program from someone. All you have to do is use e-mail! If you want to find out how, just send 'help' in the body of a mail to predictprotein@embl-heidelberg.de . I am not making advertisements - just a happy user. Enjoy! -- Kay Diederichs email: dikay@sun1.ruf.uni-freiburg.de Universitaet Freiburg, Institut fuer Biophysik, Albertstr. 23 D-79104 Freiburg, Germany Tel. +49/(0)761/2032551 FAX +49/(0)761/2032555 From owner-proteins@net.bio.net Mon Sep 13 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!gdt!bspjtpp From: bspjtpp@sunlab1.bath.ac.uk (J T P Pedersen) Newsgroups: bionet.molbio.proteins Subject: The Ponder & Richards packing prediction program Message-ID: Date: 14 Sep 93 19:14:31 GMT Organization: University of Bath, UK Lines: 20 Sender: Dr J. T Pedersen bspjtpp@uk.ac.bath.ss1 Does anyone know how one can obtain the latest Ponder & Richards packing prediction (assesment) program. The program was presented at the last School in protein design at EMBL in Heidelberg. Please let me know what the apropriate procedure is for obtaining the program if possible.... Followup-To: Distribution: Organization: School of Biological Sciences, University of Bath, UK Cc: From owner-proteins@net.bio.net Tue Sep 14 23:00:00 1993 Path: biosci!daresbury!zeta.bmc.uu.se!embl-heidelberg.de!uni-heidelberg!xlink.net!howland.reston.ans.net!wupost!medicine.wustl.edu!bcserv!ponder From: ponder@bcserv.WUSTL.EDU (Ponder (Jay)) Newsgroups: bionet.molbio.proteins Subject: Re: The Ponder & Richards packing prediction program Message-ID: <2780dnINN68v@medicine.wustl.edu> Date: 15 Sep 93 21:11:19 GMT References: Organization: Washington University School of Medicine Lines: 14 NNTP-Posting-Host: bcserv.wustl.edu The program in question was originally called PROPAK (many other folks have since played with it and some have renamed it....). A Fortran (!) version of the original that runs on most Unix workstations is available via anonymous ftp from the machine dasher.wustl.edu (128.252.162.151) in /pub/propak. A short user's manual and example output are included. Jay Ponder Biochemistry & Mol. Biophysics Washington Univ. Med. School St. Louis, MO 63110 ponder@comet.wustl.edu From owner-proteins@net.bio.net Tue Sep 14 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!warwick!nott-cs!macfd.biochem.nott.ac.uk!user From: mbxfd@unicorn.nott.ac.uk (Fergus Doherty) Newsgroups: bionet.molbio.proteins Subject: Re-constituted mitochondrial proteins? Message-ID: Date: 15 Sep 93 08:51:30 GMT Sender: news@cs.nott.ac.uk Followup-To: bionet.molbio.proteins Organization: Nottingham University, UK. Lines: 22 Nntp-Posting-Host: macfd I would like to re-constitute pure mitochondrial proteins into phospholipid vesicles. Why? Because I want to see what effect treating such vesicles with reticulocyte 15-lipoxygenase has. This enzyme oxygenates linoleic acid in phopspholipids and could lead to free-radical damage to membrane proteins. This in turn could lead to proteolysis and is the proposed mechanism for maturational loss of mitochondria from reticulocytes. So, any suggestions for candidate mito proteins? I have already chosed cytochrome c oxidase, but are there others that are readily avaialble (preferably commercially, unless you're offering!) that can be implanted into phospholipid vesicles and are active? The simpler the protein the better (cyt oxidase is in truth rather a complex multisubunit protein, but still). Any advice, suggestions gratefully received. Fergus Doherty, dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH Tel: 602 709366 FAX 602 422225 Internet: mbxfd@unicorn.nott.ac.uk From owner-proteins@net.bio.net Tue Sep 14 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!europa.eng.gtefsd.com!library.ucla.edu!news.mic.ucla.edu!unixg.ubc.ca!unixg.ubc.ca!nntp.cs.ubc.ca!news.UVic.CA!spruce.pfc.forestry.ca!PFC.Forestry.CA!AEKRAMODDOUL From: aekramoddoul@PFC.Forestry.CA (Ekramoddoullah, Abul Kalam M.) Newsgroups: bionet.molbio.proteins Subject: Re: soybean proteins Message-ID: <1993Sep14.223503.21883@spruce.pfc.forestry.ca> Date: 14 Sep 93 22:35:03 GMT References: <9309091912.AA27294@ag.auburn.edu> Sender: news@spruce.pfc.forestry.ca Reply-To: aekramoddoul@PFC.Forestry.CA Distribution: bionet Organization: Forestry Canada (Pacific Forestry Centre) Lines: 36 Nntp-Posting-Host: pfc.pfc.forestry.ca In article <9309091912.AA27294@ag.auburn.edu>, Anthony.Johnson@ag.auburn.edu (Anthony Johnson) writes: >I am working with SOYBEANS and analyzing the induction of PR PROTEINS upon infection with C. sojina using SDS-PAGE and Western blot analysis. I am trying to find anyone out there who might have any experience in this area. Any input is welcome . > Thanks > Anthony Johnson > (Auburn, AL) Because of the limitation of one-dimensional SDS-PAGE, it will be difficult to follow up the changes in protein profile of the host following pathogen infection. What reagents (specific antibodies?) are you planning to probe the Western blot. In western white pine blister rust pathosystem, we are analysing the protein profiles by two-dimensional polyacrylamide gel electrophoresis. The resolved proteins (usually 1200 proteins per sample) are quantified by laser based scanner. The statistical analysis of the data are handled with the help of a software named "PDQUEST". In the process we have developed several methodologies e.g. extraction of proteins and their determination. There is another potential problem of the ability to distingiush proteins of host and pathogen origin. To overcome this, we have now generated a series of monoclonal antibodies to the pathogen. These monoclonal antibodies will be used to detect proteins of fungal origin. If you have further question you may contact me by e-mail or phone. Abul K. M. Ekramoddoullah, Natural Resources Canada, Canadian Forest Service Pacific Forestry Centre, 506 West Burnside Rd, Victoria, B.C. Canada. Telephone (604) 363-0600 Fax (604) 363-0775 Internet: AEKRAMODDOUL@A1.PFC.Forestry.CA EKRAMODDOULLAH, ABUL KALAM M. Title: Research Scientist Forestry Canada Phone: (604) 363-0600 Victoria, B.C. Internet: AEKRAMODDOUL@A1.PFC.Forestry.CA From owner-proteins@net.bio.net Thu Sep 16 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!moe.ksu.ksu.edu!osuunx.ucc.okstate.edu!constellation!rex!cpu1.omrf.uokhsc.edu!frank From: frank@omrf.uokhsc.edu Newsgroups: bionet.molbio.proteins Subject: UV irradiation and exon splicing Message-ID: <1993Sep16.151615.1@omrf.uokhsc.edu> Date: 16 Sep 93 21:16:15 GMT Sender: news@rex.uokhsc.edu (News Admin) Organization: Oklahoma Medical Research Foundation Lines: 7 Nntp-Posting-Host: cpu1.omrf.uokhsc.edu Can anyone tell me if they know of evidence of differential gene splicing following UV irradiation? If so, how long does this effect last and what were the doses and type (or wavelength) of UV? Any references would be very helpful. Thanks in advance, Bart Frank OMRF From owner-proteins@net.bio.net Fri Sep 17 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!moe.ksu.ksu.edu!osuunx.ucc.okstate.edu!constellation!aardvark.ucs.uoknor.edu!aardvark.ucs.uoknor.edu!bfrank From: bfrank@aardvark.ucs.uoknor.edu (FRANK,BART) Newsgroups: bionet.molbio.proteins Subject: UV irradiation and exon splicing Message-ID: <17SEP199310180502@aardvark.ucs.uoknor.edu> Date: 17 Sep 93 15:18:00 GMT Organization: University of Oklahoma - University Computing Services Lines: 7 Nntp-Posting-Host: loopback.uoknor.edu News-Software: VAX/VMS VNEWS 1.41 Can anyone tell me if there have been studies showing the effects of UV-A or UV-B irradiation on differential exon splicing? Any references would be appreciated. Thnks, Bart Frank Internet: BFRANK@AARDVARK.UCS.UOKNOR.EDU From owner-proteins@net.bio.net Fri Sep 17 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!pipex!uunet!psinntp!alsys1!aecom.yu.edu!hli From: hli@aecom.yu.edu Newsgroups: bionet.molbio.proteins Subject: Who first synthesized Insulin? Message-ID: <2221@alsys1.aecom.yu.edu> Date: 18 Sep 93 01:57:03 GMT Sender: news@alsys1.aecom.yu.edu Organization: Albert Einstein College of Medicine Lines: 87 Nntp-Posting-Host: sgcr4.aecom.yu.edu From: yu31@grace.wharton.upenn.edu (Junchun Yu) Newsgroups: soc.culture.china,soc.culture.hongkong,soc.culture.taiwan Subject: Are any Chinese sci. and tech. achievements with world reputation? Message-ID: <147341@netnews.upenn.edu> Date: 15 Sep 93 20:55:04 GMT I don't care about if we Chinese have a Bethoven or a Mozart. But it is crucial for us to develop sci.and tech. (stuff deleted) I know that China claimed it was Chinese who first synthesized the artificial protein in 1958 at Beijing University. Is this claim recognized by the world biological circles? (stuff deleted) ===================end of original postiing======= 1. Science and technology, though not directly linked to arts and humanities, but its developments do reflect a nation's "taste", which is dominated by the the overall level of civilization. Thus, if you don't have Bethoven and Mozart, you can't expect a civilization haing a lot of Einstein, E. Fisher, L. Pauling, F. Sanger, et al.... 2. How about the Chinese "taste"? Best example is the story of "Chinese who first synthersized the artificial protein in 1958". Some facts: 1. the protein is insulin (from pig), which is not an inorganic compound, but a molecule from/for life. It's thought to be the smallest protein. 2. it's structure was first determined by F. Sanger in 1958(?) thus got the Nobel prize. 3. based on this development, the Chinese scientists find a chance to prove a "truth". Do you know what truth? (This reflected the Chinese "taste"!!). They wanted to prove, with latest scietific evidence, the correctness of a wrong claim by their political mentor Frederik Engels in 1800's. 4. Frederik Engels' original statement was:"protein is the most basic form of life", or something like that, which was later proved to be obvious bullshit after the discovery of nucleic acids, i.e. DNA, RNA. 5. with this knowledge already known, the scientists, best of them in China, from Shanghai Institute of Biochemistry, and Shanghai Institute of Organic Chemistry of Chinese Academy of Sciences, together with some from Department of Chemistry of Peking University started to project to waste countless badly needed money, on the journey of proving a politically important statement, yet, scientificly almost nothing because they decided to use the most stupid method to do the experiment. It started in 1958, and finished in 1966 during the Cultural Revolution, thus well-known in China :-(( Their result, they got some activity, about 30% or so, I don't remember the exact number. This number is nothing to prove anything. 6. Economically, all the efforts on this stupid project could be used to build 10 universities of top facility at Chinese level. 7. In science, this project provided no new idea nor new understanding in life, neither new development in experimental approach. It's just laborious chemical sythesis. It indeed surprized the western scientists only because no capitalist funding organization will support such stupid project in the West. Thus the socialist taste. This project by the Chinese scientists never triggered any interest in the international scientific community, never mentioned in textbook, if not for joke's sake. It was soon forgotton by even the Chinese scientists who participated in the project. If you want to visit them for the "importance" of their job, they'll be very modest, they rarely talk with you, nor to their students. 8. As you can imagine, the same project carried by an American scientist named Merrifield(sp?) even later got the Nobel Prize in 1973 for his re-sythesis of this same protein. Why? Because he turned to use a whole new method, thus very meaningful. Conclusion: The whole work by the Chinese team has been forgotton, but the method developed by the later Mr. Merrifield is still in wide use today in biochemistry lads all over the world. His method is developed into a comercial machines, so literally automated the whole process. Hope you enjoy this story. It's very sad for the Chinese scientists. BTW, the only harvest of this stupid endeavour might be that a group of scientisssts have the chance to stay in the lab instead of the field in the remote countryside in the 1960's. These people were the first to become "visiting scholars" after 1978. These people then turn back to China to teach a generation of biology students. Really a long term invest:-) From owner-proteins@net.bio.net Fri Sep 17 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!str-ccsun!dct.ac.uk!tay!growe From: growe@mcs.dundee.ac.uk (Glenn Rowe) Newsgroups: bionet.molbio.proteins Subject: Molecular design Message-ID: <1993Sep18.135934.7650@dct.ac.uk> Date: 18 Sep 93 12:59:34 GMT Organization: Maths & C.S. Dept., Dundee University, Scotland, UK Lines: 27 Nntp-Posting-Host: tay-2.mcs.dundee.ac.uk X-Newsreader: TIN [version 1.1 PL9] I'm looking for introductory/review articles describing the theory and algorithms behind computer-aided molecular design packages. The sort of thing I mean is the theory used to write a program which can test two molecules (such as a protein and a DNA segment) to find their best fit, and to see if this fit is good enough for a bond of some sort. I'm not too bothered whether I actually get a running program (though if any public domain packages exist for UNIX/Suns, I'd be interested in giving them a try): what I'm really after are the theory and algorithms behind them. Thanx. -- ______________________________________________________________ # Glenn ROWE # Tel: (0382) 23181 (x 4484) # # Dept. of Mathematics & # Fax: (0382) 201604 # # Computer Science # # # University of Dundee # # # Dundee DD1 4HN. # # # SCOTLAND. # email: growe@mcs.dund.ac.uk # -------------------------------------------------------------- "There are those who, like the author, ensconce themselves on a thunderous crag of omniscience, and with protestations of humility which are either unconvincing or totally absent, assume the obligation of appraisal, commendation, derogation or denunciation of their contemporaries. Still, by and large it is an easier job than digging a ditch." -- Jack Vance, `Star King' From owner-proteins@net.bio.net Sat Sep 18 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!sangam!vikram!imtech!mrigank From: mrigank@imtech.ernet.in (Dr. Mrigank) Newsgroups: bionet.molbio.proteins Subject: Re: Phi/Psi/Chi1 Angles from PDB Files Message-ID: <6964@imtech.ernet.in> Date: 19 Sep 93 05:44:31 GMT References: <1993Aug31.202618.16045@emba.uvm.edu> Organization: Inst. of Microbial Technology, Chandigarh, India Lines: 29 In article <1993Aug31.202618.16045@emba.uvm.edu>, mannlab@med.uvm.edu (Lab of Dr. Ken Mann) writes: > I am looking for software (Irix/VAX/MSDOS) which will find > Phi/Psi/Chi angles using PDB files. > > I really dread the thought of using a program (Alchemy/HyperChem/ > InsightII) which would require me to make these measurements > "by hand" -- that is, interactively. > > Code which automatically delivers the desired angles to standard > output would be great! > If you want a C code, there is a public domain program fisi by Rick MacDonald Univ. of Virginia rbm8p@virginia.edu If you want a Fortran code, I developed one PrtAng. If you need can contact Me. -- Dr. Mrigank \/Phone +91 172 45004 x216 Institute of Microbial Technology /\Email: mrigank@imtech.ernet.in P O Box 1304, Sector 39A \/UUCP:...!uunet!sangam!vikram!imtech!mrigank Chandigarh 160 014 India. /\ ==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+ -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From owner-proteins@net.bio.net Sun Sep 19 23:00:00 1993 Path: biosci!UNIXG.UBC.CA!flo From: flo@UNIXG.UBC.CA Newsgroups: bionet.molbio.proteins Subject: Secondary Structures from 3-D coordinates Message-ID: <9309210223.AA18787@unixg.ubc.ca> Date: 21 Sep 93 03:20:26 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 Dear Netters; Does anyone know of a program that takes 3-D coordinates of a protein, interprets secondary structures present, and outputs a linear secondary structure assignment underneath the primary sequence ? I would like to be able to compare predicted secondary structures (e.g. PredProtein server) with known secondary structure(s) of other protein(s) in a given family. I will summarize replies - Thanks in advance, Roger Graham UBC Microbiology Vancouver flo@unixg.ubc.ca From owner-proteins@net.bio.net Sun Sep 19 23:00:00 1993 Path: biosci!rutgers!gatech!howland.reston.ans.net!xlink.net!scsing.switch.ch!aristo.tau.ac.il!pc386 From: pc386@ccsg.tau.ac.il (BENNY SHOMER 9238) Newsgroups: bionet.molbio.proteins Subject: Primers database through gopher. Message-ID: <1993Sep20.174615.24886@aristo.tau.ac.il> Date: 20 Sep 93 17:46:15 GMT Sender: usenet@aristo.tau.ac.il (USENET) Organization: Tel-Aviv University Computation Center Lines: 163 X-Newsreader: TIN [version 1.2 PL1] Hello Bionetters. It has been recently suggested that a searchable database of primers for PCR will be set. The basic idea behind this database is that only ___TESTED_&_WORKING___ (!!!) primers should be contained. This may save many valuable planning and working hours, as well as money. We all know that even carefully planned primers fail to operate when it comes down to the tubes... Dan Jacobson from the Johns Hopkins Univ. GDB, and your humble servant, are now working on the establishment of this database as a gopher server. Cited below is the suggested basic form for this database. We now open a discussion regarding the suggested data fields. We are interested in hearing your opinions regarding this form. Please pay attention to the following: 1. This message has been cross posted to several bionet.xxxx groups. It is suggested however, that the thread will be maintained in bionet.molbio. methds-reagnts . This will make it easier to read and respond to everyone's followups. 2. A followup to the newsgroup is prefferred over direct responses in the Email, so as to keep the thread open. If, for any reason you want to contact us directly, Dan's address is: danj@gdb.org, my @ is: pc386@ccsg.tau.ac.il We hope that this thread will be constructive, and that the database will be 'on the air' as soon as possible. Greetings, Dan Jacobson, Benny Shomer. This is the suggested form: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Primer Name: ______________________________ Target Gene: ______________________________________________________________ Species: ___________________________ Direction: { FOR / REV } Matching Primer(s) in this database: _________________________________ Sequence (5' --> 3'): ___________________________ Length: __ Flanking bases ______ to _____ on the target sequence. Product Length (cDNA):_______ Product Length (genomic):_______ {Lengths are in bp, or 0 for inverse PCR, where length is unknown} Restriction Site Added: _____________ Mutation presented at base: __ Special Applications: { Inverse/ RT-PCR/ Sequencing/ Cloning/ Mutation/ / Ligation Mediated} __________________________________________________________________________ __________________________________________________________________________ ******************** Cycle Conditions ********************************* Hot Start: {Yes/No} Initial Denaturation- Temp: __ Time: ____ Denaturation - Temp: __ Time: ____ Annealing - Temp: __ Time: ____ Extension - Temp: __ Time: ____ Number Of Cycles: __ Final Extension - Temp: __ Time: ____ ********************** Buffer Constituents **************************** (This section basically regards non-standard buffer constituents) Reaction Volume (ul): __ Used Standard Buffer Supplied By: _______________ MgCl2 Concentration (mM): __ DMSO Concentration (%): __ Formamide Concentration (%): __ Gelatin Concentration (%): __ dNTP's Concentration (uM): __ Primers Concentration (uM): __ Polymerase Type: ___________ Polymerase Concentration (U/Rxn.): ___ Make: _____________ ************************************************************************** Submitting Author. Name: __________________________________ Institution: ______________________________________________________________ __________________________________________________________________________ Address: _________________________________________________________________ __________________________________________________________________________ E-mail : ________________________________ Fax# : ______________________ References: __________________________________________________________________________ __________________________________________________________________________ __________________________________________________________________________ Remarks: __________________________________________________________________________ __________________________________________________________________________ __________________________________________________________________________ __________________________________________________________________________ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ************************************************************** * Benny Shomer * * Tel-Aviv University * * Sackler School of Medicine, Dept.of Embryology and Teratology* *--------------------------------------------------------------* * Snail: Ramat-Aviv , Tel-Aviv 69978 , Israel. * * E-mail : pc386@ccsg.tau.ac.il * * Tel : 972-3-640-9238 FAX : 972-3-642-2046 * * * %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % So Many Computers , So Little Time ... % % % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From owner-proteins@net.bio.net Mon Sep 20 23:00:00 1993 Path: biosci!rutgers!gatech!howland.reston.ans.net!spool.mu.edu!uwm.edu!caen!uvaarpa!murdoch!darwin.clas.Virginia.EDU!rbm8p From: rbm8p@darwin.clas.Virginia.EDU (Richard Burd Macdonald) Newsgroups: bionet.molbio.proteins Subject: Read PDB ---> find Phi, Psi, etc. Message-ID: Date: 21 Sep 93 20:38:43 GMT Sender: usenet@murdoch.acc.Virginia.EDU Organization: rbmacd@athena.mit.edu Lines: 428 I've now sent corrected sifi.c code to about twenty people. I'm putting it here in the hope that someone who sees it will play with it to make it into yet another one of those too-general-to-use packages. Obviously there are plenty of folks out there who could use a fairly generic set of routines to manipulate pdb files. This program should provide enough of an example for any who thusfar have been afraid to dip their fingers into C programming. My code is not robust, but I'd be thrilled if anyone who adds to it or improves it would pass the code along. Thanks! Rick ---> Since sending this out the first time, I've found that it fails under some compilers. There is a commented line in the read_atom_record() subroutine which should help anyone who wants to fix it. -------------------------------------------------------------------- The short C program that follows calculates phi-psi and alpha-carbon bend and torsion angles for Brookhaven protein data files. The people who manage the data bank also have FORTRAN routines to do this. I have run it on SGI 4D and IBM RS6000's, but you may have to fiddle with your local math library routines. To Build: cc sifi.c -o sifi -lm Usage: sifi This routine is not particularly robust, and will fail miserably if fed anything remotely unfamiliar. /********************* CUT HERE ********************************/ /*********************************************************************** This program was written by Rick MacDonald was: University of Virginia Biophysics now: MIT Health Sciences and Technology rbm8p@virginia.edu This program will print for each amino acid residue in a pdb file: psi phi alpha carbon bend alpha carbon dihedral To Build: cc sifi.c -o sifi -lm Usage: sifi ***********************************************************************/ #include #include #define TRUE 1 #define FALSE 0 #define LINELEN 100 #define MAXATOMS 10000 #define MAXRES 1000 typedef struct { int num; char a_type[6]; char r_type[4]; char subunit; int resnum; float p[3]; /* position x,y,z */ } ATOM; typedef struct { int nitrog; int alphac; int carbon; int oxygen; char *r_type; /* 3 letter code */ char res_type; /* 1 letter code */ char subunit; float phi; float psi; float cab; float cad; int resnum; } AMINO; ATOM atom[MAXATOMS]; AMINO res[MAXRES]; int err; main(int argc, char **argv) { char *strstr(), *strncpy(), *strcat(); char *next_str(char *string); float angle(float *v1, float *v2); float dot(float *v1, float *v2); float dihedral(float *p1, float *p2, float *p3, float *p4); void cross(float *v1, float *v2, float *p); float len(float *v1); int cmpstr(char *s1, char *s2); void read_atom_record(char *rec, ATOM *atom1); char single_letter_code(char *string); register i; FILE *Fpdb; char tname[80], fname[80], line[LINELEN], *temp, WAS, WUZ, WLB; float v1[3], v2[3]; int ndx, n_atoms, n_res, rno, is, was; /*----------------------------------------------------------------------- Open file specified by command line, if it exists -----------------------------------------------------------------------*/ if(argc<2) err = printf("Usage: sifi \n"); if(argc!=2) exit(1); temp = strncpy(fname,argv[argc-1],sizeof(tname)); if ((Fpdb = fopen(fname,"r"))==NULL) err = printf("Could not open file %s\n",fname); /*----------------------------------------------------------------------- Read through the PDB format file to extract ATOM records -----------------------------------------------------------------------*/ ndx = 0; while (fgets(line,LINELEN,Fpdb)!=0) { if (strstr(line,"ATOM ")!=NULL) { read_atom_record(line,&atom[ndx]); ndx++; } } n_atoms = ndx; /*----------------------------------------------------------------------- Now we've got the ATOMs. Re-order them into residues. -----------------------------------------------------------------------*/ rno = 0; was = atom[0].resnum; for (ndx = 0; ndx < n_atoms; ndx++) { is = atom[ndx].resnum; if (is != was) rno++; if (cmpstr(atom[ndx].a_type,"CA")!=NULL) { res[rno].resnum = atom[ndx].resnum; res[rno].alphac = ndx; res[rno].r_type = atom[ndx].r_type; res[rno].subunit= atom[ndx].subunit; } else if (cmpstr(atom[ndx].a_type,"N")!=NULL) res[rno].nitrog = ndx; else if (cmpstr(atom[ndx].a_type,"C")!=NULL) res[rno].carbon = ndx; else if (cmpstr(atom[ndx].a_type,"O")!=NULL) res[rno].oxygen = ndx; was = is; } n_res = rno; /*----------------------------------------------------------------------- Find for each residue: single letter residue code phi angle psi angle cab angle = bend angle between adjacent alpha carbons cad angle = is the dihedral() or torsion angle -----------------------------------------------------------------------*/ res[0].res_type = single_letter_code(res[0].r_type); res[0].psi = -(dihedral(atom[res[1].nitrog].p, atom[res[1].alphac].p, atom[res[1].carbon].p, atom[res[2].nitrog].p)); res[1].res_type = single_letter_code(res[1].r_type); res[1].phi = -(dihedral(atom[res[0].carbon].p, atom[res[1].nitrog].p, atom[res[1].alphac].p, atom[res[1].carbon].p)); res[1].psi = -(dihedral(atom[res[1].nitrog].p, atom[res[1].alphac].p, atom[res[1].carbon].p, atom[res[2].nitrog].p)); for (rno = 2; rno <= n_res; rno++) { res[rno].res_type = single_letter_code(res[rno].r_type); res[rno].phi = -(dihedral(atom[res[rno-1].carbon].p, atom[res[rno ].nitrog].p, atom[res[rno ].alphac].p, atom[res[rno ].carbon].p)); res[rno].psi = -(dihedral(atom[res[rno ].nitrog].p, atom[res[rno ].alphac].p, atom[res[rno ].carbon].p, atom[res[rno+1].nitrog].p)); res[rno].cad = dihedral( atom[res[rno-2].alphac].p, atom[res[rno-1].alphac].p, atom[res[rno ].alphac].p, atom[res[rno+1].alphac].p); for (i=0;i<=2;i++) { v1[i] = atom[res[rno-1].alphac].p[i] - atom[res[rno].alphac].p[i]; v2[i] = atom[res[rno+1].alphac].p[i] - atom[res[rno].alphac].p[i]; } res[rno].cab = angle(v1, v2); } /*----------------------------------------------------------------------- Print this stuff out as a table. -----------------------------------------------------------------------*/ printf("%s\n", fname); printf(" # resid phi psi Cab Cat\n"); WAS = 'x'; WUZ = 'x'; WLB = res[0].subunit; res[n_res+1].subunit = 'x'; for (rno = 0; rno <= n_res; rno++) { if (res[rno].subunit != WAS) { /* This gibberish flags the meaningless */ res[rno].phi = 999.; /* values at the ends of each subunit as 999 */ } if (res[rno].subunit != WUZ) { res[rno].cab = 999.; res[rno].cad = 999.; } WUZ = WAS; WAS = res[rno].subunit; WLB = res[rno+1].subunit; if (res[rno].subunit != WLB) { res[rno].psi = 999.; res[rno].cab = 999.; res[rno].cad = 999.; } printf("%4d %c %3s %c ", res[rno].resnum, res[rno].subunit, res[rno].r_type, res[rno].res_type); printf("%5.0f ", res[rno].phi); printf("%5.0f ", res[rno].psi); printf("%5.0f ", res[rno].cab); printf("%5.0f", res[rno].cad); printf("\n"); } } /* end main */ /*********************************************************************** ***********************************************************************/ void read_atom_record(char *rec, ATOM *atom1) { char *next_str(char *string); char *ptr; float fl; ptr = rec; err = sscanf( (ptr = next_str(ptr)), "%d", &atom1->num ); err = sscanf( (ptr = next_str(ptr)), "%3s", atom1->a_type ); err = sscanf( (ptr = next_str(ptr)), "%3s", atom1->r_type ); ptr = ptr + 4; atom1->subunit = *ptr; err = sscanf( (ptr = next_str(ptr)), "%d", &atom1->resnum ); /* Remove this comment to print atom records as read from pdb printf("\n%5d %4s %s %c %d ", atom1->num, atom1->a_type, atom1->r_type, atom1->subunit, atom1->resnum); */ /* This is a silly patch --- but I can't make %Lf read a float! */ err = sscanf( (ptr = next_str(ptr)), "%f", &fl ); atom1->p[0] = fl; err = sscanf( (ptr = next_str(ptr)), "%f", &fl ); atom1->p[1] = fl; err = sscanf( (ptr = next_str(ptr)), "%f", &fl ); atom1->p[2] = fl; return; } /*********************************************************************** ***********************************************************************/ char single_letter_code(char *string) { if (cmpstr(string,"CYS")!=NULL) return 'C'; else if (cmpstr(string,"HIS")!=NULL) return 'H'; else if (cmpstr(string,"ILE")!=NULL) return 'I'; else if (cmpstr(string,"MET")!=NULL) return 'M'; else if (cmpstr(string,"SER")!=NULL) return 'S'; else if (cmpstr(string,"VAL")!=NULL) return 'V'; else if (cmpstr(string,"ALA")!=NULL) return 'A'; else if (cmpstr(string,"GLY")!=NULL) return 'G'; else if (cmpstr(string,"LEU")!=NULL) return 'L'; else if (cmpstr(string,"PRO")!=NULL) return 'P'; else if (cmpstr(string,"THR")!=NULL) return 'T'; else if (cmpstr(string,"PHE")!=NULL) return 'F'; else if (cmpstr(string,"ARG")!=NULL) return 'R'; else if (cmpstr(string,"TYR")!=NULL) return 'Y'; else if (cmpstr(string,"TRP")!=NULL) return 'W'; else if (cmpstr(string,"ASN")!=NULL) return 'N'; else if (cmpstr(string,"GLU")!=NULL) return 'E'; else if (cmpstr(string,"GLN")!=NULL) return 'Q'; else if (cmpstr(string,"LYS")!=NULL) return 'K'; else if (cmpstr(string,"ASP")!=NULL) return 'D'; return '*'; } /*********************************************************************** cmpstr does a simple compare of a string s1 with string s2 and returns a pointer to the beginning of s1 if same or NULL if not same ***********************************************************************/ int cmpstr(char *s1, char *s2) { loop: if(*s1 != *s2) return(0); if(*s1 == '\0') return(1); s1++; s2++; goto loop; } /*********************************************************************** ***********************************************************************/ char *next_str(char *string) { char c; while (((c = *string) != ' ') && (c != '\t')) string++; while (((c = *string) == ' ') || (c == '\t')) string++; return string; } /*********************************************************************** Calculate the dihedral angle between two vectors given endpoints. ***********************************************************************/ float dihedral(float *p1, float *p2, float *p3, float *p4) { void cross(float *v1, float *v2, float *p); float dot(float *v1, float *v2); float angle(float *v1, float *v2); float v1[3], v2[3], v3[3], p[3], q[3], r[3], theta; register i; for (i = 0; (i < 3); i++) { v1[i] = (p2[i] - p1[i]); v2[i] = (p2[i] - p3[i]); v3[i] = (p4[i] - p3[i]); } cross(v1,v2,p); cross(v2,v3,q); theta = angle(p,q); cross(p,q,r); if(dot(v2,r) < 0) theta = -theta; return theta; } /*********************************************************************** The vector cross product is returned as the third parameter ***********************************************************************/ void cross(float *v1, float *v2, float *p) { p[0] = (v1[1] * v2[2]) - (v1[2] * v2[1]); p[1] = (v1[2] * v2[0]) - (v1[0] * v2[2]); p[2] = (v1[0] * v2[1]) - (v1[1] * v2[0]); } /*********************************************************************** Return angle (degrees) between two vectors ***********************************************************************/ float angle(float *v1, float *v2) { float len(float *v1); float dot(float *v1, float *v2); float cos_val, sin_val, sinsq; cos_val = dot(v1,v2)/(len(v1)*len(v2)); sinsq = 1.0 - cos_val*cos_val; if( sinsq < 0.0 ) sinsq = 0.0; sin_val = sqrt(sinsq); return(atan2(sin_val,cos_val) * 57.29578); /* pi radians */ } /*********************************************************************** Return vector dot product ***********************************************************************/ float dot(float *v1, float *v2) { int i; float sum; sum = 0; for (i = 0; (i <= 2); i++) { sum = sum + (v1[i] * v2[i]); } return sum; } /*********************************************************************** Return the length of a vector ***********************************************************************/ float len (float *v1) { /* This can be faster sometimes. return ( fexp(0.5*flog ( (v1[0]*v1[0]) + (v1[1]*v1[1]) + (v1[2]*v1[2]) )) ); */ return ( sqrt ( (v1[0]*v1[0]) + (v1[1]*v1[1]) + (v1[2]*v1[2]) ) ); } From owner-proteins@net.bio.net Mon Sep 20 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!wupost!decwrl!decwrl!usenet.coe.montana.edu!news.uoregon.edu!netnews.nwnet.net!serval!bert.chem.wsu.edu!brian From: brian@bert.chem.wsu.edu (Brian W. Beck) Newsgroups: bionet.molbio.proteins Subject: Re: Secondary Structures from 3-D coordinates Message-ID: <1993Sep21.054338.10707@serval.net.wsu.edu> Date: 21 Sep 93 05:43:38 GMT References: <9309210223.AA18787@unixg.ubc.ca> Sender: news@serval.net.wsu.edu (USENET News System) Distribution: bionet Organization: Washington State University Lines: 37 X-Newsreader: TIN [version 1.2 PL0] flo@UNIXG.UBC.CA wrote: : Dear Netters; : Does anyone know of a program that takes 3-D coordinates of a protein, : interprets secondary structures present, and outputs a linear secondary : structure assignment underneath the primary sequence ? : I would like to be able to compare predicted secondary structures (e.g. : PredProtein server) with known secondary structure(s) of other protein(s) : in a given family. : I will summarize replies - Thanks in advance, : Roger Graham : UBC Microbiology : Vancouver : flo@unixg.ubc.ca Both the GCG (Genetics Computer Group) sequence analysis suite of programs, and the PSA (Protein Sequence Analysis) package by Gary Gilliland and James Jenson will output that style of data from a Chou-Fasman prediction, and GCG will also give you GOR style predictions as well. -Brian -- ============================================================================= | .---------.| Brian W. Beck | E-mail Addresses: | |/\ | ||--------------------| INTERNET brian@bert.chem.wsu.edu | || \\ WSU || Biochem/Biophysics | BITNET F0388913@WSUVMS1 | |\ - *|| WSU , 261 Fulmer | DECNET JAGUAR::F0388913 | | | || Pullman, WA | COMPUSERVE 72521,554 | | \___________|| 99164-4660 | VOICE (509)335-4083 FAX (509)335-9688| ============================================================================= From owner-proteins@net.bio.net Mon Sep 20 23:00:00 1993 Path: biosci!rutgers!flop.ENGR.ORST.EDU!gaia.ucs.orst.edu!ava.bcc.orst.edu!waterhod From: waterhod@ava.bcc.orst.edu (D_Vincent Waterhous) Newsgroups: bionet.molbio.proteins Subject: secondary structure prediction from 3D in linear display Message-ID: <27nffi$eer@gaia.ucs.orst.edu> Date: 21 Sep 93 18:00:18 GMT Distribution: na Organization: Biological Computing Consortium, OSU Lines: 34 NNTP-Posting-Host: ava.bcc.orst.edu >Subject: Secondary Structures from 3-D coordinates >Date: 21 Sep 93 03:20:26 GMT >Sender: daemon@net.bio.net >Does anyone know of a program that takes 3-D coordinates of a protein, >interprets secondary structures present, and outputs a linear secondary >structure assignment underneath the primary sequence ? >I would like to be able to compare predicted secondary structures (e.g. >PredProtein server) with known secondary structure(s) of other protein(s) >in a given family. >Roger Graham >UBC Microbiology Vancouver flo@unixg.ubc.ca In reply to the query in article 822 I would refer you to the Kabsch and Sander algorithm as described in Biopolymers (1983) 22, 2577-2637. The program is well described here and is supposedly available from the Brookhaven PDB. I have heard there are problems with the program as available from Brookhaven but I have no personal experience with it. I obtained a program written in C based on the above mentioned algorithm from Mike Carson at UAB's macromolecular crystallography group. I do not know if it is generally availble but I know that it works. You can reach Mike at carson@luna.cmc.uab.edu, and hopefully he will reply. Good luck, Vince waterhous Biophysics, Oregon State University waterhod@bcc.orst.edu From owner-proteins@net.bio.net Mon Sep 20 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pavo.csi.cam.ac.uk!camcus!owde100 From: owde100@cus.cam.ac.uk (O.W.D. Ertughrul) Newsgroups: bionet.molbio.proteins Subject: Re: Secondary Structures from 3-D coordinates Message-ID: <1993Sep21.083425.26941@infodev.cam.ac.uk> Date: 21 Sep 93 08:34:25 GMT References: <9309210223.AA18787@unixg.ubc.ca> Sender: news@infodev.cam.ac.uk (USENET news) Distribution: bionet Organization: U of Cambridge, England Lines: 19 Nntp-Posting-Host: bootes.cus.cam.ac.uk Molecular Simulation's QUANTA will do this for you under its "protein design" menus. It will display a rotatable alpha carbon backbone in colours corresponding to secondary structural elements and displays the primary sequence in appropriate colours above the structure. Orhan. ****************************************************************************** Orhan W.D. Ertughrul University of Cambridge St. Edmund's College Department of Biochemistry Cambridge CB3 OBN Tennis Court Road Cambridge CB2 1QW e-mail : owde100@cus.cam.ac.uk From owner-proteins@net.bio.net Mon Sep 20 23:00:00 1993 Path: biosci!rutgers!gatech!howland.reston.ans.net!agate!ames!network.ucsd.edu!clinical-mac-86.ucsd.edu!user From: dkolk@popmail.ucsd.edu (Dan Kolk) Newsgroups: bionet.molbio.proteins Subject: Help: Supershifting bZIP protein in EMSA Message-ID: Date: 21 Sep 93 17:22:17 GMT Followup-To: bionet.molbio.proteins Organization: UCSD School of Medicine Lines: 8 NNTP-Posting-Host: clinical-mac-86.ucsd.edu I am attempting to supershift a bZIP protein that we have cloned. We know the antibody is good ( it works in western blots and in immunoprecipitations.) I have had no luck. Are there any good references out there for supershifts? How much antibody do you added the reaction mixture? How long do you incubate it? Do you alter the reaction conditions? Any advice would be appreciated. From owner-proteins@net.bio.net Tue Sep 21 23:00:00 1993 Path: biosci!rutgers!sgigate!olivea!charnel!yeshua.marcam.com!news.kei.com!sol.ctr.columbia.edu!howland.reston.ans.net!agate!doc.ic.ac.uk!uknet!comlab.ox.ac.uk!gjb From: gjb@bioch.ox.ac.uk (Geoff Barton) Newsgroups: bionet.molbio.proteins Subject: Re: Secondary Structures from 3-D coordinates Message-ID: <1993Sep22.172418.18631@geoff.bioch.ox.ac.uk> Date: 22 Sep 93 17:24:18 GMT References: <9309210223.AA18787@unixg.ubc.ca> Distribution: bionet Organization: Department of Biochemistry, University of Oxford Lines: 7 Originator: gjb@geoff.biop You need DSSP from Chris Sander at EMBL. I think the program is available on the EMBL file server. See the paper: Kabsch and Sander (1983) Biopolymers, 22, 2577-2637 Geoff From owner-proteins@net.bio.net Tue Sep 21 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: wti%rxvlab.dnet@com.smithkline (wti) Newsgroups: bionet.molbio.proteins Subject: Free hydrazide groups Message-ID: <1993Sep22.073811.11247@gserv1.dl.ac.uk> Date: 22 Sep 93 07:18:40 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 16 Precedence: first-class Original-To: "proteins@dl.ac.uk" <"proteins@dl.ac.uk"%INET.dnet@smithkline.com> Original-Cc: WTI@smithkline.com. Dear protein members, We perform protein-polysaccharide coupling, where hydrazide groups from ADH on the PS react with COOH groups on the protein in presence of EDC. The problem lies in the determination of residual free hydrazides after coupling, and, if any, the capping or removal of these groups, and all this in presence of the free amine groups of the protein, who interfere in the assays and capping reactions. Any usefull suggestions or references are mostly wellcome. You can also contact me for further information. You can mail me through the proteins list, or direct at my address. from: Wim Tiest at Smithkline Beecham Rixensart Belgium internet: WTI%RXVLAB.dnet@smithkline.com I Thank you very much!! From owner-proteins@net.bio.net Wed Sep 22 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!noc.near.net!saturn.caps.maine.edu!dartvax!grafton.dartmouth.edu!knight From: knight@grafton.dartmouth.edu (John Boswell) Newsgroups: bionet.molbio.proteins Subject: National Biomedical ESR Center Address? Message-ID: Date: 23 Sep 93 20:56:11 GMT Sender: news@dartvax.dartmouth.edu (The News Manager) Organization: Dartmouth College, Hanover, NH Lines: 15 Hi, Could someone please tell me the email or ftp address of the National Biomedical ESR Center in Milwaukee? I'd like to use a few of their EPR programs, but I can't find an address (gopher wasn't much help). I could send some USnail, but I was hoping for an email address. Along the same lines, the address for the Illinois Electron Spin Resonance Center would be very helpful as well :) thanks a bunch, -John Boswell -- **************************************************************************** Dr. John Boswell knight@grafton.dartmouth.edu Dept. of Chemistry, Biochemistry and Molecular Biology Oregon Graduate Institute, Portland, OR 503-690-1086 From owner-proteins@net.bio.net Wed Sep 22 23:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!uknet!pavo.csi.cam.ac.uk!mbfs.bio.cam.ac.uk!seb1005 From: seb1005@mbfs.bio.cam.ac.uk (Steven Brenner) Newsgroups: bionet.molbio.proteins Subject: Re: Secondary Structures from 3-D coordinates Message-ID: <1993Sep23.103243.23430@infodev.cam.ac.uk> Date: 23 Sep 93 10:32:43 GMT References: <9309210223.AA18787@unixg.ubc.ca> <1993Sep22.172418.18631@geoff.bioch.ox.ac.uk> Sender: news@infodev.cam.ac.uk (USENET news) Distribution: bionet Organization: U of Cambridge, England Lines: 29 Nntp-Posting-Host: mbfs.bio.cam.ac.uk gjb@bioch.ox.ac.uk (Geoff Barton) writes: >You need DSSP from Chris Sander at EMBL. I think the program is available >on the EMBL file server. >See the paper: Kabsch and Sander (1983) Biopolymers, 22, 2577-2637 DSSP will nominally provide the desired output, but its assignments of secondary structure frequently disagree with those of those who solved the structure. There are many reasons for this (many of them not DSSP's fault), but mainly it appears to be a consequence of DSSPs simple algorithm for determining secondary structure. Therefore, it may also be worth looking at VADAR, which performs the same task using somewhat more sophisticated criteria. The program was developed by David Wishart at U Alberta. The program can be found at canopus.biochem.ualberta.ca as pub/VadarAug93.tar.Z Steven P.S. DSSP may be found on ftp.embl-heidelberg.de in the directory pub/databases/protein_extras/dssp. Source code is available by signing the license agreement; executables are found in that directory. -- Steven E. Brenner | Department of Biochemistry seb1005@mbfs.bio.cam.ac.uk | University of Cambridge Lab +44 223 333671 | Tennis Court Road Fax +44 223 333345 | Cambridge CB2 1QW, UK From owner-proteins@net.bio.net Thu Sep 23 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!rpi!utcsri!utnut!torn!nott!emr1!weathere From: weathere@emr1.emr.ca (Carl Weatherell) Newsgroups: bionet.molbio.proteins Subject: Collagen-Metal Complexes Message-ID: <1993Sep24.154114.28046@emr1.emr.ca> Date: 24 Sep 93 15:41:14 GMT Organization: Dept. of Energy, Mines, and Resources, Ottawa Lines: 13 X-Newsreader: TIN [version 1.1 PL8] In a solution of low pH (1-4) why would Co be preferentially complex with collagen or collagen fragments vs Cu or Zn?? What may the complex be?? Background; 1-10 ppm collagen in 180 g/L H2SO4, 50g/L Zn current density 450 A/m2, 1-10 ppm Co and Cu If anyone decides to respond and needs further information, please let me know. Carl weathere@emr1.emr.ca From owner-proteins@net.bio.net Fri Sep 24 23:00:00 1993 Path: biosci!rutgers!usc!math.ohio-state.edu!uwm.edu!post.its.mcw.edu!not-for-mail From: simhan@post.its.mcw.edu (Dr. C. Narasimhan) Newsgroups: bionet.molbio.proteins Subject: ESR Address Message-ID: <281fla$qq3@post.its.mcw.edu> Date: 25 Sep 93 13:04:42 GMT Organization: Medical College of Wisconsin; Milwaukee Wisconsin Lines: 2 NNTP-Posting-Host: post.its.mcw.edu X-Newsreader: TIN [version 1.2 PL1] National Biomedical ESR Center, 8701 Watertown Plank Rd., Milwaukee, WI 53226. Tel: (414)266-4000. Contact: Dr. Chris Felix From owner-proteins@net.bio.net Sat Sep 25 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!spool.mu.edu!olivea!news.bbn.com!hsdndev!dartvax!grafton.dartmouth.edu!knight From: knight@grafton.dartmouth.edu (John Boswell) Newsgroups: bionet.molbio.proteins Subject: Re: National Biomedical ESR Center Address? Message-ID: Date: 26 Sep 93 16:58:08 GMT References: <1993Sep24.225852.9516@news.gdb.org> Sender: news@dartvax.dartmouth.edu (The News Manager) Organization: Dartmouth College, Hanover, NH Lines: 11 Hi, Thanks to everyone who sent me info on ESR address. I'll try to thank everyone individually, but in case I miss someone- thanks! have a good day, -John Boswell -- Dr. John Boswell knight@grafton.dartmouth.edu Oregon Graduate Institute, Portland, OR 503-690-1086 From owner-proteins@net.bio.net Sat Sep 25 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!news.gdb.org!dev.gdb.org!danj From: danj@dev.gdb.org (Dan Jacobson) Newsgroups: bionet.molbio.proteins Subject: Re: National Biomedical ESR Center Address? Message-ID: <1993Sep24.225852.9516@news.gdb.org> Date: 24 Sep 93 22:58:52 GMT References: Sender: news@news.gdb.org Organization: Johns Hopkins University Genome Data Base (GDB) Lines: 52 Nntp-Posting-Host: dev.gdb.org In article knight@grafton.dartmouth.edu (John Boswell) writes: >Hi, > Could someone please tell me the email or ftp address of the >National Biomedical ESR Center in Milwaukee? I'd like to use a few of their >EPR programs, but I can't find an address (gopher wasn't much help). I >could send some USnail, but I was hoping for an email address. > Along the same lines, the address for the Illinois Electron Spin >Resonance Center would be very helpful as well :) > Well I can tell you that the director of the National biomedical ESR center is James Hyde: HYDE, JAMES S MEDICAL COLLEGE OF WISCONSIN 8701 WATERTOWN PLANK RD MILWAUKEE, WI 53226 I can't pull up his phone or email - but someone who does ESR work there is: William E Antholine (414) 257-8296. ------------------- For the Illinois Electron Spin Resonance Center: BELFORD, R LINN UNIVERSITY OF ILLINOIS 505 SOUTH MATHEWS AVENUE URBANA, IL 61801 I have a bit more information on this one: name: belford r linn email: belford@rlb6000.scs.uiuc.edu phone: (217) 333-2553 Best of luck, Dan Jacobson danj@mail.gdb.org From owner-proteins@net.bio.net Sun Sep 26 23:00:00 1993 Path: biosci!rutgers!netnews.upenn.edu!biochem.dental.upenn.edu!ellis From: ellis@biochem.dental.upenn.edu (Ellis Golub) Newsgroups: bionet.molbio.proteins Subject: reconstruction of 3D coordinates Message-ID: <150040@netnews.upenn.edu> Date: 27 Sep 93 16:00:56 GMT Sender: news@netnews.upenn.edu Organization: University of Pennsylvania Lines: 17 Nntp-Posting-Host: biochem.dental.upenn.edu Keywords:crystal structure stereo coordinate Has anyone used Rossmann's program, stereo, recently to reconstruct 3D coordinates from 2D stereo images? I would appreciate help, advice or clues to more recent software/hardware for this purpose. Thanks, Ellis Golub ============================================================================== Ellis Golub Phone: (215) 898-4629 Biochemistry Department FAX: (215) 898-3695 University of Pennsylvania ellis @ biochem.dental.upenn.edu School of Dental Medicine 4001 Spruce Street Philadelphia, PA 19104-6003 =============================================================================== From owner-proteins@net.bio.net Sun Sep 26 23:00:00 1993 Path: biosci!bloom-beacon.mit.edu!gatech!howland.reston.ans.net!pipex!uknet!warwick!not-for-mail From: lsrgn@csv.warwick.ac.uk (Peter Willingmann) Newsgroups: bionet.molbio.proteins Subject: what means NTCB Message-ID: <286ssi$75f@violet.csv.warwick.ac.uk> Date: 27 Sep 93 14:21:06 GMT Organization: Computing Services, University of Warwick, UK Lines: 18 NNTP-Posting-Host: violet.csv.warwick.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Greetings Netters, Can anybody give me some advice what NTCB means? I found the name in the GCG packages in the program peptidesort Any input will be much appreciated. Mail to me or answer to this news-group. Thank you and all the best peter peter willingmann lsrgn@csv.warwick.ac.uk Department of Biological Sciences Unniversity of Warwick From owner-proteins@net.bio.net Sun Sep 26 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!pipex!warwick!not-for-mail From: lsrgn@csv.warwick.ac.uk (Peter Willingmann) Newsgroups: bionet.molbio.proteins Subject: re NTCB... thanks Message-ID: <287fci$1f8@violet.csv.warwick.ac.uk> Date: 27 Sep 93 19:36:50 GMT Organization: Computing Services, University of Warwick, UK Lines: 15 NNTP-Posting-Host: violet.csv.warwick.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Greetings Netters, I was asking what is NTCB?.... I get in three hours 5 answers and all pointing to 2-nitro-5-thiocyanobenzoic acid.... to make chemical cleavage at cysteine. I know it has to do with protein/peptid sequence analysis.... but my memory dont served me..... Thank you very much for the prompt responses. Indeed the internet is really great.... Best of luck peter From owner-proteins@net.bio.net Sun Sep 26 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: emrasmus@dk.aau.biobase (Erik Michael Rasmussen) Newsgroups: bionet.molbio.proteins Subject: Re: what means NTCB Message-ID: <1993Sep27.154549.12373@gserv1.dl.ac.uk> Date: 27 Sep 93 15:44:34 GMT References: <9392715250.~INN-AAAa25923.bionet-news@dl.ac.uk>; from "Peter Willingmann" at Sep 27, 93 3:21 pm Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 22 Precedence: first-class Original-To: lsrgn@csv.warwick.ac.uk Original-Cc: proteins@uk.ac.daresbury X-Mailer: ELM [version 2.3 PL11] > > Greetings Netters, > > Can anybody give me some advice what NTCB means? > I found the name in the GCG packages in the program > peptidesort > Any input will be much appreciated. Mail to me or > answer to this news-group. > Thank you and all the best > > peter > > Could it be 2-nitro-5-thiocyanobenzoic acid used to make chemical cleavage at cysteine. Michael Erik Michael Rasmussen phone (+45) 35322100 Department of Genetics E-mail emrasmus@biobase.aau.dk Institute of Molecular Biology University of Copenhagen From owner-proteins@net.bio.net Sun Sep 26 23:00:00 1993 Path: biosci!ARTHUR.CITI2.FR!SZAJNERT From: SZAJNERT@ARTHUR.CITI2.FR Newsgroups: bionet.molbio.proteins Subject: Database of protein-binding DNA motifs Message-ID: <1993Sep27.104137.7770@gserv1.dl.ac.uk> Date: 27 Sep 93 10:41:34 GMT Sender: kristoff@net.bio.net Reply-To: SZAJNERT@ARTHUR.CITI2.FR Distribution: bionet Lines: 9 Hello, Iam looking for database(s) of protein-binding DNA motifs.I will appreciate some help. Thanks to everybody in advance.My address is: szajnert@frciti51.bitnet. Bye! Marie-France Szajnert INSERM U129 75014 Paris France From owner-proteins@net.bio.net Mon Sep 27 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!sangam!vikram!imtech!mrigank From: mrigank@imtech.ernet.in (Dr. Mrigank) Newsgroups: bionet.molbio.proteins Subject: Re: Molecular design Message-ID: <7062@imtech.ernet.in> Date: 26 Sep 93 16:44:01 GMT References: <1993Sep18.135934.7650@dct.ac.uk> Organization: Inst. of Microbial Technology, Chandigarh, India Lines: 56 In article <1993Sep18.135934.7650@dct.ac.uk>, growe@mcs.dundee.ac.uk (Glenn Rowe) writes: > I'm looking for introductory/review articles describing the theory > and algorithms behind computer-aided molecular design packages. > The sort of thing I mean is the theory used to write a program > which can test two molecules (such as a protein and a DNA segment) to > find their best fit, and to see if this fit is good enough for a bond > of some sort. I'm not too bothered whether I actually get a running > program (though if any public domain packages exist for UNIX/Suns, I'd > be interested in giving them a try): what I'm really after are the > theory and algorithms behind them. Thanx. Hi I put a list of references cosidered good. List is not comprehensive but will be usefull. o "Reviews in Computational Chemistry" by Lipkowitz and Boyd, Vol I-IV. o Boyd and Lipkowitz (J. Chem. Edu. 1982, 59, 269-274. o Lou Allinger and Phil Bowen Reviews of Computational Chemistry (vol 2, Chapter 3). o Mike Cory and Phil Bowen Encyclopedia of Pharmaceutical Technology (vol 3, 1991 by Marcel Dekker, Inc.). o A.I. Hopfinger (J. Med. Chem. 1985, 28, 1133). o Ira N. Levine, Quantum Mechanics, 4th ed, pp 583-587, o A Handbook of Computational Chemistry, by Tim Clark; o Ulrich Burkert and Norman L. Allinger, Molecular Mechanics, ACS Monograph 177, American Chemical Society, Washington, D.C., 1982 (about 340 pages). o "Computational Chemistry Using the PC", By Donald Rodgers, VCH, 1991. o P. Cox, J. Chem. Ed.,59, (1982), pp275-277. o "Conformational Properties of Macromolecules" by A. Hopfinger Academic press, o "Computer Software Applications in Chemistry" by Peter C. Jurs. o "Comprehensive Medicinal Chemistry", edited by Corwin Hansch and John Sammes. Vol 4 George Seibel and Peter Kollman Hope this will help. -- Dr. Mrigank \/Phone +91 172 45004 x216 Institute of Microbial Technology /\Email: mrigank@imtech.ernet.in P O Box 1304, Sector 39A \/UUCP:...!uunet!sangam!vikram!imtech!mrigank Chandigarh 160 014 India. /\ ==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+ -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From owner-proteins@net.bio.net Mon Sep 27 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!library.ucla.edu!news.mic.ucla.edu!unixg.ubc.ca!unixg.ubc.ca!cellcx.nce.ubc.ca!user From: gilkes@unixg.ubc.ca Newsgroups: bionet.molbio.proteins Subject: Re : Secondary Structures... Summary Message-ID: Date: 28 Sep 93 01:17:46 GMT Followup-To: bionet.molbio.proteins Organization: The University of British Columbia Lines: 69 NNTP-Posting-Host: cellcx.nce.ubc.ca Q. Does anyone know of a program that takes 3-D coordinates of a protein, interprets secondary structures present, and outputs a linear secondary structure assignment underneath the primary sequence ? I would like to be able to compare predicted secondary structures (e.g. PredProtein server) with known secondary structure(s) of other protein(s) in a given family. Thanks to all who send replies to this query. Suggestions follow : 1. Both the GCG (Genetics Computer Group) sequence analysis suite of programs, and the PSA (Protein Sequence Analysis) package by Gary Gilliland and James Jenson will output that style of data from a Chou-Fasman prediction, and GCG will also give you GOR style predictions as well. Brian W. Beck brian@bert.chem.wsu.edu 2. Molecular Simulation's QUANTA will do this for you under its "protein design" menus. It will display a rotatable alpha carbon backbone in colours corresponding to secondary structural elements and displays the primary sequence in appropriate colours above the structure. Orhan W.D. Ertughrul e-mail : owde100@cus.cam.ac.uk 3. Try DSSP written by, I think Kabsch/Sander. For more information look: Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features. Wolfgang KABSCH and Chris SANDER (1983), Biopolymers Vol. 22, 2577-2637. In the paper they explain how they recognize secondary structure based on combinations of bond angles, H-bonding etc. The program is available at the anonymous ftp-server at EMBL-Heidelberg. Ready to run versions for various machine-types can be found in /pub/software/unix/dssp (SGI, SUN, EVS, DEC, VMS). Source code is available by signing the license agreement; executables are found in in the directory pub/databases/protein_extras/dssp. The program is also available from Chris Sander (e-mail: Sander@EMBL-Heidelberg.DE) Hannes Floeckner; peter (Sibbald@EMBL-Heidleberg.DE) DSSP will nominally provide the desired output, but its assignments of secondary structure frequently disagree with those of those who solved the structure. There are many reasons for this (many of them not DSSP's fault), but mainly it appears to be a consequence of DSSPs simple algorithm for determining secondary structure. Therefore, it may also be worth looking at VADAR, which performs the same task using somewhat more sophisticated criteria. The program was developed by David Wishart at U Alberta. The program can be found at canopus.biochem.ualberta.ca as pub/VadarAug93.tar.Z Steven E. Brenner seb1005@mbfs.bio.cam.ac.uk 4. MolViewer will read a 3d structure (connectivity information must also be present) and give you a list of backbone dihedrals which would be easy to convert to 2ndary struct. However, it runs only under NeXTStep (ie, on a NeXT or a 486 running NeXTStep). 5. I don't know the software used to generate the information, but the Brookhaven database entries contain helix, sheet, and turn assignments as part of their ".ent" files. The information is not strictly linear, as helicies are grouped first, then all residues in sheets, then turns, but residue numbers are provided in every case. As a last resort, you could even sort the data by hand, however it shouldn't take more than a small program (even in BASIC if necessary) to sort out the information. Note that specialized structures are mentioned in the REMARKS section of the .ent files. Also, the Brookhaven Database is available on CDROM. Stephen Aley saley@ucsd.edu From owner-proteins@net.bio.net Mon Sep 27 23:00:00 1993 Path: biosci!lhc!darwin.sura.net!udel!gatech!concert!news-feed-1.peachnet.edu!athena.cs.uga.edu!dogwood!watson From: watson@dogwood.botany.uga.edu (Mark Watson) Newsgroups: bionet.molbio.proteins Subject: Reference for pulse-chase Message-ID: <2887tk$h4f@athena.cs.uga.edu> Date: 28 Sep 93 02:35:32 GMT Distribution: na Organization: uga Lines: 9 NNTP-Posting-Host: dogwood.botany.uga.edu Hello Netreaders, I have been trying to find a good reference for analyzing pulse chase experimental data. e.g. calculating turnover, half-life, ect. Any refernces that may help would be appreciated. (most of the papers I've found using this technique don't cite their reference and I've seemed to have misplaced any classroom notes I may have taken on the subject many moons ago) Thanks, Mark Watson Watson@dogwood.botany.uga.edu From owner-proteins@net.bio.net Wed Sep 29 23:00:00 1993 Path: biosci!MINNA.ACC.IIT.EDU!CMSMUELLER From: CMSMUELLER@MINNA.ACC.IIT.EDU Newsgroups: bionet.molbio.proteins Subject: transfer proteins from a stained gel Message-ID: <01H3K44Z5NWM8ZF3FO@minna.acc.iit.edu> Date: 30 Sep 93 16:52:33 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 8 Help!! Does anyone know how to transfer protein from a gel to nitrocellulose after it has been stained with Coomassie blue? We need to perform a Western analysis but do not have any more of the sample. Thanks David Mueller Chicago Medical School From owner-proteins@net.bio.net Wed Sep 29 23:00:00 1993 Path: biosci!NBRF.GEORGETOWN.EDU!POSTMASTER From: POSTMASTER@NBRF.GEORGETOWN.EDU Newsgroups: bionet.molbio.proteins Subject: Announcement of Interruption of Access to PIR Message-ID: <01H3K2VVI0J6AOM16S@NBRF.Georgetown.Edu> Date: 30 Sep 93 15:18:09 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 21 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 Friday 1 October. From 16:00 EDT Friday 1 October through about 16:00 EDT Saturday 2 October it will not be possible for users to access the Protein Identification Resource Network Server, the On-line System, or contact the PIR staff by electronic mail. While the system will be accessible until the scheduled downtime, it may not be possible to access some or all of the sequence databases. We regret any inconvenience this temporary loss of service may 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 Thu Sep 30 23:00:00 1993 Path: biosci!daresbury!daresbury!news From: emrasmus@dk.aau.biobase (Erik Michael Rasmussen) Newsgroups: bionet.molbio.proteins Subject: Re: transfer proteins from a stained gel Message-ID: <1993Oct1.090109.6212@gserv1.dl.ac.uk> Date: 1 Oct 93 08:59:37 GMT References: <9393018019.~INN-LBAa29713.bionet-news@uk.ac.daresbury>; from "CMSMUELLER@MINNA.ACC.IIT.EDU" at Sep 30, 93 4:52 pm Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 25 Precedence: first-class Original-To: CMSMUELLER@MINNA.ACC.IIT.EDU Original-Cc: proteins@uk.ac.daresbury X-Mailer: ELM [version 2.3 PL11] > > Help!! Does anyone know how to transfer protein from > a gel to nitrocellulose after it has been stained with > Coomassie blue? We need to perform a Western > analysis but do not have any more of the sample. > > Thanks > David Mueller > Chicago Medical School > My guess is that if it is still wet, my suggetion is to equilibrate the gel in transferbuffer and and run the blotting. If the transfer is succesful you will see it right away because the comassie will remain on the proteins. It's just to try. I haven't tried myself, but I will be very interested in if it is possible, because I could fear that the proteins is too fixed in the gel. Michael Erik Michael Rasmussen phone (+45) 35322100 Department of Genetics E-mail emrasmus@biobase.aau.dk Institute of Molecular Biology University of Copenhagen From owner-proteins@net.bio.net Thu Sep 30 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!uunet!usc!math.ohio-state.edu!news.acns.nwu.edu!network.ucsd.edu!pravda.sdsc.edu!genie.sdsc.edu!surles From: surles@genie.sdsc.edu (Mark Surles) Newsgroups: bionet.molbio.proteins,bionet.software Subject: Phi/psi to cartesian Message-ID: <28dpkp$6n6@pravda.sdsc.edu> Date: 30 Sep 93 05:08:41 GMT Organization: San Diego Supercomputer Center @ UCSD Lines: 14 Xref: biosci bionet.molbio.proteins:899 bionet.software:6026 NNTP-Posting-Host: genie.sdsc.edu I want to generate an 'idealized' poly-alanine given a long series of phi/psi angles. I am looking for code, a code fragment, or algorithm that will take a list of phi/psi angles, not necessarily repeating, and produce cartesian coordinates of all the atoms. This is not too hard, but my brain is not working tonight, and I'm sure someone has done this already. Thanks, Mark Surles surles@sdsc.edu San Diego Supercomputer Center