From owner-bio-matrix@net.bio.net Mon Sep 02 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Alexy Eroshkin Newsgroups: bionet.molbio.bio-matrix Subject: Protein Multiple Sequences Editor on IuBio FTP-server Date: 3 Sep 1996 11:20:14 +0100 Organization: State Research Center of Virology & Biotechnology VECTOR Lines: 51 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <50h0ou$83l@mserv1.dl.ac.uk> Original-To: bio-matrix@dl.ac.uk To: bio-matrix@dl.ac.uk From: eroshkin@vector.nsk.su Subject: Protein Multiple Sequences Editor on IuBio FTP-server Dear All, ProMSED, Protein Multiple Sequences EDitor for MS Win 3.x/95 is available now from IuBIO software library: ftp://iubio.bio.indiana.edu/molbio/ibmpc/promsed1.exe (as self-extracted archive). ProMSED is an easy-to-use application for automatic and manual multiple protein sequences alignment, alignment editing, analysis and printing. Interface and the main functions are similar to Microsoft Word. ProMSED can align complete set of sequences, its subset and any selected block, providing thus flexible tool for sequences analysis, visualization, edition and illustrations preparation. Some features: o reads five sequence formats (NBRF/PIR, Pearson (Fasta), EMBL/SwissProt, Intelligenetics and CLUSTAL) and combines sequences from different files; o automatic multiple sequence alignment with ClustalV algorithm; o single and multiple sequence input and edit; o manual alignment includes sequences grouping, blocks deleting, pasting, etc.; o visual analysis is facilitated by amino amino acid coloring reflecting aa similarity in physico-chemical, mutational and other properties; o option for interactive alignment in selected block, leaving unchanged previously aligned regions; o outputs alignment in two formats, produces publication quality alignments; o loads several protein families into different windows; o a HELP is included; Special thanks to Dr. Desmond Higgins for source code of ClustalV. Demo version has limits on length and number of sequences. Comments, bug reports and suggestions for new features are welcome and should be sent by email to eroshkin@vector.nsk.su. Inquiries can be addressed to: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Alexey Eroshkin Institute of Molecular Biology E.mail: eroshkin@vector.nsk.su State Research Center of Virology and Tel: +7 (3832) - 647774 Biotechnology "Vector" Fax: +7 (3832) - 328831 Koltsovo, Novosibirsk Region 633159 Russia ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-bio-matrix@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!CCR.DSI.UANL.MX!pearl From: pearl@CCR.DSI.UANL.MX ("Dr. Paul R.Earl") Newsgroups: bionet.molbio.bio-matrix Subject: Biomx, new electronic journal in English & Spanish Date: 5 Sep 1996 12:51:34 -0700 Organization: UANL Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <322F4C1A.357C@ccr.dsi.uanl.mx> NNTP-Posting-Host: net.bio.net Computerizing Biology (or the students!) is an important area for us. Making teaching easier is too. Please see http://www.uanl.mx/biomx or simply enter Biomx under Yahoo search. Thank you. Dr Paul R Earl From owner-bio-matrix@net.bio.net Wed Sep 04 23:00:00 1996 Path: biosci!biosci!not-for-mail From: Iosif Vaisman Newsgroups: bionet.general,bionet.biophysics,bionet.molbio.proteins,bionet.molec-model,bionet.molbio.methds-reagnts,bionet.software,bionet.structural-nmr,bionet.xtallography,bionet.cellbiol,bionet.jobs,bionet.software.gcg,bionet.molbio.bio-matrix Subject: Computational Molecular Biology Workshop, October 15-19, 1996 Date: 5 Sep 1996 15:03:54 -0700 Organization: The University of North Carolina at Chapel Hill Lines: 47 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.general:23165 bionet.biophysics:2276 bionet.molbio.proteins:8677 bionet.molec-model:1132 bionet.molbio.methds-reagnts:48854 bionet.software:16470 bionet.structural-nmr:1480 bionet.xtallography:2850 bionet.cellbiol:5405 bionet.software.gcg:1978 bionet.molbio.bio-matrix:755 CAROLINA WORKSHOPS University of North Carolina at Chapel Hill Computational Molecular Biology October 15 - 19, 1996 This course is designed for scientists with limited prior experience in computational molecular biology. The topics to be covered include: biomolecular informatics and databases, protein and nucleic acid sequence analysis and alignment, 3D protein structure analysis and prediction, molecular modeling and dynamic simulations of proteins and nucleic acids, and structure-based drug design. The workshop will consist of the in-depth theoretical lectures and intensive hands-on laboratory sessions. CAROLINA WORKSHOPS are intensive hands-on courses designed to teach cutting edge methods in molecular biology and biotechnology. Four or five courses on different topics in molecular biology and/or biotechnology are offered each year. The courses are designed for novice students as well as for individuals with prior experience. All students benefit from in-depth interaction with instructors. To apply, send a curriculum vitae and a brief letter describing your research interests and their relevance to the Workshop. Applicants should contact the program office as soon as possible. Please indicate your complete mailing address and telephone/fax number. Application Deadline-September 7, 1996. Tuition - $ 1,200.00. Participation is limited to 15 people. COURSE DIRECTOR: Alexander Tropsha, Ph.D., University of North Carolina at Chapel Hill INSTRUCTORS: Frank K. Brown (Oxford Molecular) David C. Richardson (Duke University) Wayne Litaker (UNC-Chapel Hill) Alexander Tropsha (UNC-Chapel Hill) Michael Mitchell (UNC-Chapel Hill) Iosif I. Vaisman (UNC-Chapel Hill) For further information or to apply, contact: Dr. Wayne Litaker, Facility Director University of North Carolina at Chapel Hill Program in Molecular Biology & Biotechnology 442 Taylor Hall CB 7100 Chapel Hill, North Carolina 27599-7100 TELEPHONE (919) 966-1730, FAX (919) 966-6821 E-MAIL litaker@med.unc.edu From owner-bio-matrix@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Alexy Eroshkin Newsgroups: bionet.molbio.bio-matrix Subject: ANNOUNCE ProAnalyst -- new software for protein/peptide analysis Date: 9 Sep 1996 11:49:00 +0100 Organization: State Research Center of Virology & Biotechnology VECTOR Lines: 112 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <510sms$idh@mserv1.dl.ac.uk> Original-To: bio-matrix@dl.ac.uk To: bio-matrix@dl.ac.uk From: eroshkin@vector.nsk.su Subject: ANNOUNCE ProAnalyst - new software for protein/peptide analysis --------------------------------------- ProAnalyst - PROTEIN ANALYST (ver 1.02) --------------------------------------- State Research Center of Virology and Biotechnology Koltsovo, Novosibirsk Region, 633159 Russia and Vladimir Ivanisenko with Alexey Eroshkin are pleased to announce the availability of an easy-to-use, state-of-the-art MS-DOS application designed to solve traditional and new tasks of protein science. ProAnalyst FEATURES: - includes intuitive user interface to facilitate data analysis; - inputs single and multiple protein sequences, activity/property/ genotype data, protein 3D structures; - relates experimental data to protein primary and tertiary structure; - finds sites influencing protein activity/property; - finds relationships between protein sites' characteristics (hydrophobicity, amphipathicity, etc.) and protein activities; - investigates differences between proteins divided by functional, evolutionary or other criteria (for example, relates genotype to phenotype); - investigates physico-chemical factors related with activity changes in a set of mutant proteins (including multiple physico-chemical factors); - simulates protein-engineering experiments and predicts activity of mutant protein; - searches motifs and patterns in combinatorial libraries (peptide and phage-displayed libraries); - provides linear correlation and multiple linear regression analysis, discriminant, ANOVA and alphabetical analysis; - classic profile/plot analysis for a single sequence (hydrophobicity, helical amphipathicity, etc.) suplemented with average, min, max and dispresion plots for a set of sequences; - searches regions with high and low variability of physico-chemical characteristics; - calculates structure-activity correlation profile; - performs cross and inter-group variability analysis based on several matrices of amino acid similarity; - main part of methods works with sequential and spatial sites; - maps obtained results onto 3D structure; - sorts sequences by activity, group number, motifs found; - visualizes multiple alignments and protein 3D structures (stereo) with sites highlighted; - has data converter from several protein sequence formats (FASTA, SWISS-PROT, CLUSTAL, PIR, IG); - has data bases with 50 aligned protein families, more than 60 amino acid properties, HELP, Manual and examples with program applications. ProAnalyst MAY BE USEFUL: - for chemists and biochemists making investigations of protein structure-function and structure-activity analysis; - for protein engineers trying to improve some protein properties; - for molecular biologists that need to get sense from multiple protein alignments and to analyze complicated combinatorial libraries; - for geneticists studying phenotype-genotype correlations; - for those who need color protein 3D pictures with sites highlighted; - for students in any field of PROTEIN SCIENCE; - for those who interested in comparative protein sequence analysis. PUBLICATIONS: 1. Eroshkin A.M., Zhilkin P.A., Fomin V.I. Algorithm and computer program PROANAL for analysis of relationship between structure and activity in a family of proteins or peptides. CABIOS, 1993, 9, 491-497. 2. Eroshkin A.M., Minenkova O.O., Fomin V.A., Ivanisenko V.A., Ilyichev A.A. Analysis of peptide fragment insertions into major coat protein of bacteriophages M13, f1 and fd. Relation of protein structural characteristics and viability of mutant phages. Molec. Biology (Russia), 1993, 27, 1345-1355. 3. Eroshkin A.M., Fomin V.I., Zhilkin P.A., Ivanisenko V.A., Kondrakhin Y.V. PROANAL version 2: multifunctional program for analysis of multiple protein sequence alignments and studying structure-activity relationships in protein families. CABIOS, 1995, 11, 39-44. 4. Kuzmicheva G.A., Kuvshinov V.N., Razumov I.A., Ivanisenko V.A., Eroshkin A.M., et al. Mapping of group specific hemagglutinating antigenic epitope of alphavirus envelope protein E2 using phage display. Doklady Academii Nauk RAN, in press. 5. Morozov B.M., Ivanisenko V.A., Eroshkin A.M., Ugarova N.N. Analysis of relations between bioluminescence color and the structure of beetle luciferases: identification of the sites influencing bioluminescence color. Molec. Biology (Russia), in press. AVAILABILITY: ProAnalyst is available from EBI software library: ftp://ftp.ebi.ac.uk/pub/software/dos/proanalyst/ (as self-extracted archive). Current version works with up to 15 sequences. The length of sequences must be less than or equal to 5000. Comments, bug reports, suggestions for new features are welcome and should be sent by e-mail to: salex@vector.nsk.su (Vladimir Ivanisenko) or eroshkin@vector.nsk.su (Alexey Eroshkin) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Alexey Eroshkin Institute of Molecular Biology E.mail: eroshkin@vector.nsk.su State Research Center of Virology and Tel: +7 (3832) - 647774 Biotechnology "Vector" Fax: +7 (3832) - 328831 Koltsovo, Novosibirsk Region 633159 Russia ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-bio-matrix@net.bio.net Sun Sep 08 23:00:00 1996 Path: biosci!ihnp4.ucsd.edu!gondor!newsfeeder.sdsu.edu!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!howland.erols.net!newsfeed.internetmci.com!sierra.net!news.sierra.net!news From: "Marc C. Brande, MS, Founder" Newsgroups: bionet.molbio.bio-matrix Subject: Free Brochure: Cell Bio/Imaging Services at Your Site Date: Mon, 09 Sep 1996 13:57:05 +0000 Organization: Cultured Cell Systems (619) 587-4830 FAX: (619) 552-1516 (www.bio.com/co/css.html) (Hands-On As-Needed Cell Biology/Imaging Expertise at Your Site) Lines: 1 Message-ID: <32342231.1A03@sierra.net> Reply-To: mcbrande@sierra.net NNTP-Posting-Host: bigchief-d29.sierra.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Macintosh; U; 68K) Email your Full Name/Address/FAX to: mcbrande@sierra.net From owner-bio-matrix@net.bio.net Wed Sep 11 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!nntp.primenet.com!news.mindspring.com!uunet!in2.uu.net!inet.guthrie.org!nschang!nschang From: nschang@inet.guthrie.org (Nan-Shan Chang) Newsgroups: bionet.molbio.bio-matrix Subject: Postdoctoral Position Open Followup-To: bionet.molbio.bio-matrix Date: Thu, 12 Sep 96 00:36:31 GMT Organization: Guthrie HealthCare System Lines: 8 Distribution: world Message-ID: NNTP-Posting-Host: gw.guthrie.org X-Newsreader: VersaTerm Link v1.1.5 Postdoctoral / Research Associate Position is available at the Guthrie Research Institute to participate in the molecular characterization of extracellular matrix signal in conferring cancer cell resistance to tumor necrosis factor and apoptosis (JBC 270, 7765, 1995). Experience in molecular cloning, sequencing, expression and/or background in immunology is required. Send curriculum vitae and 3 reference letters to: Dr. N.-S. Chang, Guthrie Research Institute, 1 Guthrie Square, Sayre, PA 18840. Fax: (717)882-5151. Email: nschang@inet.guthrie.org An Equal Opportunity Employer. From owner-bio-matrix@net.bio.net Wed Sep 11 23:00:00 1996 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!news.sgi.com!www.nntp.primenet.com!nntp.primenet.com!news.mindspring.com!uunet!in2.uu.net!inet.guthrie.org!nschang!nschang From: nschang@inet.guthrie.org (Nan-Shan Chang) Newsgroups: bionet.molbio.bio-matrix Subject: Postdoctoral Position Open Followup-To: bionet.molbio.bio-matrix Date: Thu, 12 Sep 96 00:40:23 GMT Organization: Guthrie HealthCare System Lines: 9 Distribution: world Message-ID: NNTP-Posting-Host: gw.guthrie.org X-Newsreader: VersaTerm Link v1.1.5 Postdoctoral / Research Associate Position is available at the Guthrie Research Institute to participate in the molecular characterization of extracellular matrix signal in conferring cancer cell resistance to tumor necrosis factor- and Fas-mediated apoptosis (JBC 270, 7765, 1995; BBRC, in press, 1996). Experience in molecular cloning, sequencing, expression and/or background in immunology is required. Send curriculum vitae and 3 reference letters to: Dr. N.-S. Chang, Guthrie Research Institute, 1 Guthrie Square, Sayre, PA 18840. Fax: (717)882-5151. Email: nschang@inet.guthrie.org An Equal Opportunity Employer. From owner-bio-matrix@net.bio.net Sat Sep 14 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.bio-matrix Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 15 Sep 1996 02:00:36 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 239 Sender: daemon@net.bio.net Distribution: world Message-ID: <199609150900.CAA13233@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-bio-matrix@net.bio.net Sun Sep 15 23:00:00 1996 Path: biosci!BIOINFORMATICS.WEIZMANN.AC.IL!lvrebhan From: lvrebhan@BIOINFORMATICS.WEIZMANN.AC.IL (Michael Rebhan) Newsgroups: bionet.molbio.bio-matrix Subject: New protein database at Weizmann Date: 16 Sep 1996 11:03:49 -0700 Organization: Weizmann Institute of Science, Bioinformatics Unit Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <323D978E.59E2@bioinformatics.weizmann.ac.il> NNTP-Posting-Host: net.bio.net At the Bioinformatics Server of the Weizmann Institute of Science in Rehovot, Israel, you can find a new database covering many aspects of proteins and other molecules, including their cellular function, a list of antibodies, email addresses of researchers, and their involvement in diseases (http://bioinformatics.weizmann.ac.il/hotmolecbase). Because the author (http://bioinformatics.weizmann.ac.il/hotmolecbase/rebhan.html), unfortunately, is able to invest only a small proportion of his time into this project, the list of entries is still relatively small. However, he would be very glad if some people could be interested in supporting this project (writing something not too time-consuming about their molecule of interest, reviewing information about certain molecules, suggesting sources for funding etc.). If you want to get an idea about the basic concept of this database, have a look at the typical entry at: http://bioinformatics.weizmann.ac.il/hotmolecbase/entries/tau.htm Comments and suggestions to: lvrebhan@bioinformatics.weizmann.ac.il From owner-bio-matrix@net.bio.net Mon Sep 16 23:00:00 1996 Path: biosci!ARIEL.UCS.UNIMELB.EDU.AU!horaitis From: horaitis@ARIEL.UCS.UNIMELB.EDU.AU (Rania Horaitis) Newsgroups: bionet.molbio.bio-matrix Subject: (none) Date: 16 Sep 1996 18:44:51 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 3 Sender: daemon@net.bio.net Distribution: world Message-ID: <01I9L1HTUGLU00RP0D@muwayb.ucs.unimelb.edu.au> NNTP-Posting-Host: net.bio.net unsubscribe horaitis@ariel.ucs.unimelb.edu.au From owner-bio-matrix@net.bio.net Tue Sep 17 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Alexy Eroshkin Newsgroups: bionet.molbio.bio-matrix Subject: ProMSED (alignment editor) for Eastern Hemisphere on NSC-server Date: 18 Sep 1996 11:16:21 +0100 Organization: State Research Center of Virology & Biotechnology VECTOR Lines: 30 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <51oi5l$sfv@mserv1.dl.ac.uk> Original-To: bio-matrix@dl.ac.uk To: bio-matrix@dl.ac.uk From: eroshkin@vector.nsk.su Subject: ProMSED (alignment editor) for Eastern Hemisphere on NSC-server To make ProMSED easier available in Eastern Hemisphere it is installed at Novosibirsk Scientific Center FTP-server: ftp://ftp.bionet.nsc.ru/pub/biology/vector/promsed.dem/promsed$.exe (as self-extracted archive). ProMSED, Protein Multiple Sequences EDitor for MS Windows 3.x/95, is an easy-to-use application for automatic and manual multiple protein sequences alignment, alignment editing, analysis and printing. Interface and main functions are similar to Microsoft Word. ProMSED can align complete set of sequences, any subset or selected block. Features: reads five sequence formats; combines sequences from different files; automatic alignment with ClustalV algorithm; amino acid coloring by their similarity in physico-chemical, mutational and other specified properties; interactive alignment in selected block; outputs alignment in two formats; loads several protein families into different windows; etc. The length and number of sequences are limited in this version. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Alexey Eroshkin Institute of Molecular Biology E.mail: eroshkin@vector.nsk.su State Research Center of Virology and Tel: +7(3832) - 647774 Biotechnology "Vector" Fax: +7 (3832) - 328831 Koltsovo, Novosibirsk Region 633159 Russia ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-bio-matrix@net.bio.net Wed Sep 18 23:00:00 1996 Path: biosci!daresbury!not-for-mail From: Alexy Eroshkin Newsgroups: bionet.molbio.bio-matrix Subject: ProMSED (protein alignment editor) for Eastern Hemisphere on NSC-server Date: 19 Sep 1996 11:35:37 +0100 Organization: State Research Center of Virology & Biotechnology VECTOR Lines: 30 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <51r7lp$n8k@mserv1.dl.ac.uk> Original-To: biomatrx@dl.ac.uk To: biomatrx@dl.ac.uk From: eroshkin@vector.nsk.su Subject: ProMSED (protein alignment editor) for Eastern Hemisphere on NSC-server To make ProMSED easier available in Eastern Hemisphere it is installed at Novosibirsk Scientific Center FTP-server: ftp://ftp.bionet.nsc.ru/pub/biology/vector/promsed.dem/promsed$.exe (as self-extracted archive). ProMSED, Protein Multiple Sequences EDitor for MS Windows 3.x/95, is an easy-to-use application for automatic and manual multiple protein sequences alignment, alignment editing, analysis and printing. Interface and main functions are similar to Microsoft Word. ProMSED can align complete set of sequences, any subset or selected block. Features: reads five sequence formats; combines sequences from different files; automatic alignment with ClustalV algorithm; amino acid coloring by their similarity in physico-chemical, mutational and other specified properties; interactive alignment in selected block; outputs alignment in two formats; loads several protein families into different windows; etc. The length and number of sequences are limited in this version. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Alexey Eroshkin Institute of Molecular Biology E.mail: eroshkin@vector.nsk.su State Research Center of Virology and Tel: +7(3832) - 647774 Biotechnology "Vector" Fax: +7 (3832) - 328831 Koltsovo, Novosibirsk Region 633159 Russia ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-bio-matrix@net.bio.net Mon Sep 30 23:00:00 1996 Path: biosci!agate!howland.erols.net!EU.net!Norway.EU.net!online.no!nntp-oslo.UNINETT.no!nntp-trd.UNINETT.no!daresbury!not-for-mail From: Alexy Eroshkin Newsgroups: bionet.molbio.bio-matrix Subject: ANNOUNCE ProAnWin: protein alignment & structure-activity analysis Date: 1 Oct 1996 11:47:24 +0100 Organization: State Research Center of Virology & Biotechnology VECTOR Lines: 262 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <52qsrs$o1u@mserv1.dl.ac.uk> Original-To: biomatrx@dl.ac.uk To: biomatrx@dl.ac.uk From: Alexey Eroshkin Subject: ANNOUNCE ProAnWin: protein alignment and structure-activity analysis ************************************** ProAnWin - Protein Analyst for Windows ************************************** State Research Center of Virology and Biotechnology Koltsovo, Novosibirsk Region, 633159 Russia and Irina Pika, Anatoly Frolov, Vladimir Ivanisenko with Alexey Eroshkin are pleased to announce the availability of new MS Windows application for multiple protein sequence alignment, comparative sequences analysis, studying protein structure-activity (property/genotype) relationships and designing site-directed mutagenesis. DESCRIPTION: ProAnWin studies the relationships between protein/peptide activity (or property or related phenotype) and characteristics of some regions in primary or tertiary structure of these molecules. Structure-activity analysis is based on the sequences of protein family, data on protein activity (pK, ED50, Km or any other) and, if available, 3D structure of one of these proteins (supposing the common 3D fold for all the homologs). The main aim is to find out the factors responsible for the variation of protein activities: location of activity-modulating site and important structural characteristics of the site. The program makes the following: input of sequences from several formats (SWISS-PROT, PIR, FASTA, GCG, CLUSTAL) and 3D structure in PDB format; flexible multiple protein sequences alignment and threading sequences into known 3D structure (ClustalV + manual alignment); input of user-defined protein activities, properties or related phenotypes (with possibility to transform activity: log(x), 1/x, etc.); calculation of many characteristics (hydrophobicity, amphipathicity, etc.) of linear and spatial protein sites; fast multiple (up to eight independent factors) linear regression analysis of structure-activity relationships; activity prediction for untested or mutated proteins; data visualization (regression plots, 3D pictures with sites highlighted, multiple alignments); displaying found sites on sequences and 3D structure. The program has two main related windows - with protein sequences and with 3D structure; any site highlighted in sequences is highlighted in 3D structure and vise versa. ProAnWin aligns complete set of sequences, subset or any selected block, providing thus possibility for iterative alignment that preserve some previously found blocks or those imposed from some biological data (active center, catalytic residues). The program can be applied to analysis of various protein-related biological data, to prediction of activity (phenotype) of newly sequenced proteins and to simulation of protein-engineering experiments. DATA EXAMPLES: 1. The family of disintegrins (proteins from snake venom) with tested activity. Name Sequence (part) Activity* 41 51 61 71 81 Trigramin alpha QCGEGLCCDQCSFIEEGTVCRIARGDDLDDYCNGRSAGCPRNP 130 Albolabrin .............MKK..I..R............I........ 222 Elegantin ..AD.......R.KKKR.I..R....NP..R.T.Q..D....G 136 Flavoridin ..AD.......R.KKKTGI.......FP..R.T.L.ND...WN 100 Batroxastatin ..A........R.KGA.KI..R....NP..R.T.Q..D....R 133 Applagin ..A........L.MK.....-R.....VN.....I........ 50 Kistrin ........E..K.SRA.KI...P...MP..R.T.Q..D...YH 128 Echistatin alpha E.ES.P..RN.L.LK...I.LR.....M......LTCP..... 56 Bitistatin ..NH.E.....K.KKAR.........WN....T.K.SD..W.H 237 Bitan alpha ..NH.E.....R.KKA..........WN....T.K.SD..W.H 108 * - Activity is measured as the concentration of protein (in nM) required to 50% attenuation of platelet-rich plasma aggregation stimulated by adenosine-diphosphate. 2. The set of synthetic peptides with tested antimicrobial activity Name Activity* Peptide sequence Analog A2 400 GIHYLSHKSFSKFFAGVGKFTNS Analog A1 100 GIHYLSHKSFSKFFAGVQKFTNS Antisense P 60 GIHYLSHKSFSKFFCGVQKFTNS Analog B1 40 GIHYLSHKSFSKFFKGVQKFTNS Analog B2 40 GIHYLSHKSFSKFFKGVGKFTNS Magainin 2 20 GIGKFLHSAKKFGKAFVGEIMNS Analog C1 20 GIHKLSHKSFSKFFKGVQKFTNS Analog C2 20 GIHKLSHKSFSKFFKGVGKFTNS Analog P1 10 AIHNFAHKSFAKFFRAVKKFANA Analog P2 5 AIHNLAHKSLAKLLRAVKKLANA Analog P3 5 GIHNFAHKSFAKFFRAVKKFANS Analog M2 3 KIHKLAHKLLKKLLKAVKKLAKA * - Minimal inhibitory concentration (in mcg/ml) against E.coli 3. The set of unrelated peptides with tested immunogenicity. ------------------------------------------------- Protein Oncogene Sequence Immuno- region genicity* ------------------------------------------------- 409-425 C-SRC RLIEDNEYTARQGAKFP 4 468-482 C-SRC NREVLDQVERGYRMP 4 499-508 C-SRC WRRDPEERPT 4 001-018 V-KI-RAS MTEYKLVVVGASGVGKSA 5 119-135 V-KI-RAS DLPSRTVDTKQAQELAR 5 161-175 V-KI-RAS REIRQYRLKKISKEE 2 001-018 V-HA-RAS MTEYKLVVVGARGVGKSA 4 001-018 C-HA(EJ)-RAS MTEYKLVVVGAVGVGKSA 3 001-018 C-HA-RAS MTEYKLVVVGAGGVGKSA 5 029-044 V-HA-RAS VDEYDPTIEDSYRKQV 4 091-108 V-HA-RAS EDIHQYREQIKRVKDSDD 4 126-136 V-HA-RAS ESRQAQALARS 4 146-155 V-HA-RAS AKTRQGVEDA 5 160-179 V-HA-RAS VREIRQHKLRKLNPPDESGP 5 011-024 V-MYB PQESSKAGPPSGTT 4 033-047 V-MYB MAFAHNPPAGPLPGA 3 146-162 V-MYB DNTRTSGDNAPVSCLGE 4 168-186 V-MYB PSPPVDHGCLPEESASPAR 4 170-185 V-MYB PPVDHGCLPEESASPA 2 247-260 V-MYB PFHKDQTFTEYRKM 4 247-265 V-MYB PFHKDQTFTEYRKMHGGAV 4 541-555 V-FES RHSTSSSEQEREGGR 4 584-593 V-FES PEVQKPLHEQ 4 782-796 V-FES FLRTEGARLRMKTLL 4 840-846 V-FES SREAADG 0 893-905 V-FES ASPYPNLSNQQTR 3 901-913 V-FES NQQTREFVEKGGR 4 222-234 V-MYC PPTTSSDSEEEQE 0 323-334 V-MYC RTLDSEENDKRR 4 340-350 V-MYC ERQRRNELKLR 4 363-371 V-MYC NNEKAPKVV 1 389-403 V-MYC RLIAEKEQLRRRREQ 4 395-405 V-MYC EQLRRRREQLK 4 400-406 V-MYC RREQLKH 0 * logarithm of antipeptide antibody titers. 4. Phenotype-genotype correlations. Influenza A virus M2 protein from strains sensitive (labeled "sen") and resistant to amantadine or rimantadine ("res"). Strain Sensitivity Sequence (N-terminal part only) PR8-34 res MSLLTEVETPIRNEWGCRCNGSSDPLAIAANIIGILHLILWILDR MON88 res ....................D.................T...... LEN3-83 res ..........................T...........T...... MOS88 res ..........................T...........T...... MON86 res ..........................T...........T...... SVER82 res ..........................T...........T...... WS33 res ....................D.....V.................. LEN85 res ....................D.....VV................. WSN33 res ....................D....FV.................. LEN49 res ....................D.....VV..........T...... LEN6-83 res ....................D...S.VV..S.............. SWONT81 res ....................D.....VA..S.............. SW29-37 res ....................D.....VA..S.............. SWIA30 res ..........T.........D.....VA..S.............. SWWIS61 res ..........T.S.......D.....VA..S.............. SWIA88 res .................K..D.....VAV.S.............. AA60 sen ....................D.....VV..S.............H KOREA68 sen ....................D.....VV..S......F....... BANG79 sen ....................D.....VV..S.............. FW50 sen ....................D.....VV..S.............. MEM88 sen ....................D.....VV..S.............. USSR77 sen .............Q......D.....VV..S.............. PINALB79 sen ..........T..G.E.K.SD.....V...S.............. SWHK82 sen ..........T..G.E.K.SD.....V...S.............. SWNED85 sen ..........T..G....FSD.....V...S.............. FPVR34 sen ..........T..G.E....D.....I...S............N. MLRDNY78 sen ..........T..G.E.K.SD.....V...S.............. TYMN81 sen ..........T..G.E.K.SD.....V...S.............. TYMN80 sen ..........T..G.E.K.SD.....V...S.............. CKVIC85 sen ..........T..G.E.K.SD.....V...S.............. ProAnWin IS USEFUL IN: - protein structure-function and structure-activity investigations; - designing proteins and peptides with improved activity; - making multiple protein alignments and getting sense from it; - studying phenotype-genotype correlations; - preparation of protein 3D pictures with sites highlighted; - comparative protein sequence analysis. AVAILABILITY: ProAnWin is available (as self-extracted archive) from EBI software library: ftp://ftp.ebi.ac.uk/pub/software/dos/proanwin and, in Eastern Hemisphere, from NSC software library: ftp://ftp.bionet.nsc.ru/pub/biology/vector/proanwin.dem/paw$.exe The version is limited in number of analyzed sequences. INSTALLATION: The files required to run ProAnWin are distributed in the form of a single compressed file. Create a directory "PROANWIN" in your hard disk, for example, C. Copy the file to the directory, run the file from DOS prompt and answer Yes to all questions. To start the program run PROAWIN.EXE from windows. PROGRAM CONTENT: Directory: Main directory - program modules DATA - examples of data and output files; amino acid physico-chemical properties (>50); manual ALIGNS - 50 aligned protein family sequences PUBLICATIONS: 1. Eroshkin A.M., Zhilkin P.A., Fomin V.I. Algorithm and computer program PROANAL for analysis of relationship between structure and activity in a family of proteins or peptides. CABIOS, 1993, 9, 491-497. 2. Eroshkin A.M., Minenkova O.O., Fomin V.A., Ivanisenko V.A., Ilyichev A.A. Analysis of peptide fragment insertions into major coat protein of bacteriophages M13, f1 and fd. Relation of protein structural characteristics and viability of mutant phages. Molec. Biology (Russia), 1993, 27, 1345-1355. 3. Eroshkin A.M., Fomin V.I., Zhilkin P.A., Ivanisenko V.A., Kondrakhin Y.V. PROANAL version 2: multifunctional program for analysis of multiple protein sequence alignments and studying structure-activity relationships in protein families. CABIOS, 1995, 11, 39-44. 4. Morozov B.M., Ivanisenko V.A., Eroshkin A.M., Ugarova N.N. Analysis of relations between bioluminescence color and the structure of beetle luciferases: identification of the sites influencing bioluminescence color. Molec. Biology (Russia), in press. Comments, bug reports, suggestions for new features are welcome and should be sent by e-mail to: Alexey Eroshkin OTHER TOOLS AVAILABLE: ProAnalyst, Multifunctional analysis of protein sequences and structures (MS-DOS version of ProAnWin with additional functionality: searching motifs, physico-chemical plots, alphabetical and physico-chemical analysis of protein sequence variation, structure-activity determination profile, etc.): IUBio archive: ftp://iubio.bio.indiana.edu/molbio/ibmpc/panalys1 EMBL library: ftp://ftp.ebi.ac.uk/pub/software/dos/proanalyst NSC library: ftp://ftp.bionet.nsc.ru/pub/biology/vector/proanaly.dem/panalys$ ProMSED, Protein Multiple Sequences EDitor for MS Windows 3.x/95 ("a la" Word for Windows style + ClustalV + manual alignment + amino acid coloring + more): EMBL library: ftp://ftp.ebi.ac.uk/pub/software/dos/promsed NSC library: ftp://ftp.bionet.nsc.ru/pub/biology/vector/promsed.dem/promsed$ IUBio archive: ftp://iubio.bio.indiana.edu/molbio/ibmpc/promsed1 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Alexey Eroshkin Institute of Molecular Biology E.mail: eroshkin@vector.nsk.su State Research Center of Virology and Tel: +7 (3832) - 647774 Biotechnology "Vector" Fax: +7 (3832) - 328831 Koltsovo, Novosibirsk Region 633159 Russia ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++