From owner-chemistry@ccl.net Sat Jun 29 05:57:10 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id FAA11264; Sat, 29 Jun 1996 05:08:29 -0400 (EDT) Received: from risc1.lrm.fi.cnr.it for antonio@risc1.lrm.fi.cnr.it by bedrock.ccl.net (8.7.5/950822.1) id FAA12530; Sat, 29 Jun 1996 05:08:28 -0400 (EDT) Received: by risc1.lrm.fi.cnr.it (AIX 3.2/UCB 5.64/4.03) id AA20960; Sat, 29 Jun 1996 10:06:17 +0200 Date: Sat, 29 Jun 1996 10:06:17 +0200 From: antonio@risc1.lrm.fi.cnr.it (Antonio Rosato) Message-Id: <9606290806.AA20960@risc1.lrm.fi.cnr.it> To: chemistry@ccl.net Subject: Protein Interaction & molecular dynamics Dear Netters, I would like to know whether programs exist (either free or commercial) which perform molecular dynamics with the aim of simulating protein-protein recognition. Should this be brownian dynamics? Protocols for performing such studies with an "ordinary" molecular dynamics program (e.g. AMBER, CHARMM...) are welcome as well Thanks to all! Antonio e-mail: antonio@risc1.lrm.fi.cnr.it From xiang@auriga.rose.brandeis.edu Sat Jun 29 13:57:14 1996 Received: from auriga.rose.brandeis.edu for xiang@auriga.rose.brandeis.edu by www.ccl.net (8.7.5/950822.1) id NAA12638; Sat, 29 Jun 1996 13:26:22 -0400 (EDT) Received: by auriga.rose.brandeis.edu (5.57/Ultrix3.0-C) id AA09966; Sat, 29 Jun 96 13:26:22 -0400 Date: Sat, 29 Jun 96 13:26:22 -0400 From: xiang@auriga.rose.brandeis.edu (Phil Xiang) Message-Id: <9606291726.AA09966@auriga.rose.brandeis.edu> To: chemistry@www.ccl.net Subject: RE: CLL:bioinformatics group? >>Does any body know if there is an internet discussion group for bioinformatics? >What area of bioinformatics are you interested in?? > >Michael N. Liebman, Ph. D. >Director, Bioinformatics >Vysis, Inc. >3100 Woodcreek Drive >Downers Grove, Illinois 60515 > >(708) 271-7190 office area code will become 630 on August 1 >(708) 271-7008 fax >************************************* >please note new e-mail address mliebman@vysis.com >************************************* Bioinformatics is computation for the purpose of constructing and interpreting genome. As a subdiscipline of biology, it contributes to the understanding of life by intimate interactions with all other subdisciplines of biology, including genetics, molecular biology, structural biology, biochemistry. The first logical task of bioinformatics is to construct the entire physical map of a genome from pieces called the EST, in a procedure known as genome mapping. The main purpose here is to organize the immense amount of data and to avoid repetitive work. The second task of bioinformatics is to identify genes, or exons, from the noncoding parts, or introns. This is possible based on the belief that genes are subject to constraints during evolution and should therefore have features different from noncoding regions which are not subject to evolutionary constraints. The third task is to tell the function of a gene from its sequence and to predict how mutations affect function. It is believed that functionally related proteins either evolve >from common ancesters or have converged during evolution so that they share common features in either sequence or structure. The common approaches to discovering sequence similarities are: homology search, pattern/motif search, amino acid composition analysis. The common approaches to discovering structural similarities are: secondary structure prediction, structural classification, inverse folding (threading, fold recognition), multiple alignment, homology modeling. The forth task is to understand how a set of genes work in concert at the organismal level. The purpose here is to understand at a quantitative level processes such as expression/controll/regulation, signal transduction, biochemical pathways, development, adaptation, evolution. This is the most exciting part of bioinformatics and my understanding is that the work has just begun. Concepts/Algorithms: physical map, ORF, intron/exon, homology, fold classes, dynamic programming, Smith-Waterman/Needleman-Wunsch, threading, 3D profiles, knowledge-based potentials, secondary structure prediction, fold recognition, pattern/motif, scoring matrices, alignment, Z score, twilight zone, phylogenetic tree, neural nets, genetic algorithm. Databases: GenBank, SwissProt, PIR, PDB, EMBL, GDB, ProSite, ProDom, SCOP, HSSP/FSSP, ExPASY. Programs: GeneFind, GCG, BLAST, FASTA, Entrez, OWL, Pileup, ProfileSearch, CLUSTAL. Computer tools: Relational database, SQL, Sybase, Oracle, C/C++, Client/Server, distributed computing, HTML/WWW, cgi, Java, Perl. The above delineation no doubt reflects my biases and may have missed some major marks and as such is only intended to serve as a lead for discussion. I am very interested in hearing other points of view. I am especially interested in hearing from industry people what skills/talents are hot there. Phil Xiang Biophysics,Brandeis University,(617)736-4906 http://www.rose.brandeis.edu:80/users/xiang/