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<h2> <table style="MARGIN-TOP: 0pt; LINE-HEIGHT: 100%; BORDER-COLLAPSE: collapse" cellspacing="1" cellpadding="0" width="680" bgcolor="#eeeeff" summary="" border="1"> <tbody> <tr> <td align="center" width="99" bgcolor="#ccffee" height="28"> <p style="MARGIN-TOP: 0pt; MARGIN-BOTTOM: 0pt; LINE-HEIGHT: 80%" align="center"><a href="http://psibase.kobic.re.kr"><font face="Times New Roman" color="#999999" size="3"><big><strong><span class="external"><font color="#800080">PSIbase server</font></span></strong></big> </font></a></p> </td> <td align="center" width="85" bgcolor="#99ffee" height="28"> <p style="MARGIN-TOP: 0pt; MARGIN-BOTTOM: 0pt; LINE-HEIGHT: 80%" align="center"><font face="Times New Roman" color="#999999" size="3"><big><strong><font color="#800080">[[Publication]]</font></strong></big></font></p> </td> <td align="center" width="120" bgcolor="#ccffee" height="28"> <p style="MARGIN-TOP: 0pt; MARGIN-BOTTOM: 0pt; LINE-HEIGHT: 80%" align="center"><font face="Times New Roman" color="#ffffdd" size="3"><strong><a class="external" title="http://bio.cc" rel="nofollow" href="http://bio.cc/">BiO center</a></strong></font></p> </td> <td align="center" width="128" bgcolor="#99ffdd" height="28"> <p style="MARGIN-TOP: 0pt; MARGIN-BOTTOM: 0pt; LINE-HEIGHT: 80%" align="center"><font face="Times New Roman" color="#ddeeff" size="3"><big><a class="external" title="http://bio.cc/Biosite/Mediawiki" rel="nofollow" href="http://biosite.org">BioSite</a></big> </font></p> </td> <td align="center" width="120" bgcolor="#ccffee" height="28"> <p style="MARGIN-TOP: 0pt; MARGIN-BOTTOM: 0pt; LINE-HEIGHT: 80%" align="center"><font face="Times New Roman" color="#ffffdd" size="3"><big><strong>[[Download]] </strong></big></font></p> </td> </tr> </tbody> </table> <p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px; LINE-HEIGHT: 100%" align="left"><strong><font face="Times New Roman" size="7"><br /> </font></strong></p> <p style="MARGIN-TOP: 0px; MARGIN-BOTTOM: 0px; LINE-HEIGHT: 100%" align="left"><strong><font face="Times New Roman" size="7">P</font><font face="Times New Roman" color="#006699" size="7">S</font><font face="Times New Roman" color="#0099cc" size="7">I</font><font face="Times New Roman" color="#ffcc66" size="7">M</font><font face="Times New Roman" color="#ff6633" size="7">A</font><font face="Times New Roman" color="#cc0033" size="7">P </font><font face="Times New Roman" color="#cc0033" size="4">:</font><font face="Times New Roman" color="#cc0033" size="7"> </font><font face="Times New Roman" color="#003300" size="6">p</font><font face="Times New Roman" color="#cc0033" size="4">rotein </font><font face="Times New Roman" color="#0033cc" size="6">s</font><font face="Times New Roman" color="#cc0033" size="4">tructural </font><font face="Times New Roman" color="#3399cc" size="6">i</font><font face="Times New Roman" color="#cc0033" size="4">nteractome </font><font face="Times New Roman" color="#ff9900" size="6">m</font><font face="Times New Roman" color="#ff6600" size="6">a</font><font face="Times New Roman" color="#cc0033" size="6">p</font></strong></p> <br /> About PSIMAP</h2> <p>PSIMAP is a tool and DB for constructing interactomes. It is a general protocol of mapping proteins and their family interactions. The first map created was called 'pdb-sin' as it was based on PDB database (PDB structural interaction network). It was the first protocol that could map the global molecular interactions using protein domain (family) structural folds. </p> <ul> <li>[[Development history of PSIMAP]] </li> </ul> <div class="editsection" style="FLOAT: right; MARGIN-LEFT: 5px">[<a title="PSIMAP" href="http://bio.cc/PSIMAP/Mediawiki/index.php?title=PSIMAP&action=edit&section=2">edit</a>]</div> <h2>PSIMAP and its sub projects </h2> <ul> <li><a class="external" title="http://interactomics.org" rel="nofollow" href="http://interactomics.org/">Interactome project</a><span class="urlexpansion"> (<em>http://interactomics.org</em>)</span> </li> <li><a class="external" title="http://humaninteractome.net" rel="nofollow" href="http://humaninteractome.org">Human Interactome Project</a><span class="urlexpansion"> (<em>http://humaninteractome.org</em>)</span> </li> <li><a href="http://psibase.kobic.re.kr"><span class="external"><font color="#800080">PSIBASE</font></span></a><span class="urlexpansion"> (<em>http://psibase.kobic.re.kr</em>)</span> </li> <li><a class="external" title="http://interpare.net" rel="nofollow" href="http://interpare.net/">Interpare project</a><span class="urlexpansion"> (<em>http://interpare.net</em>)</span> </li> </ul> <div class="editsection" style="FLOAT: right; MARGIN-LEFT: 5px">[<a title="PSIMAP" href="http://bio.cc/PSIMAP/Mediawiki/index.php?title=PSIMAP&action=edit&section=3">edit</a>]</div> <h2>Publication of PSIMAP related papers </h2> <ol> <li>Jefferson, E. R., Walsh, T. P. and Barton, G. J. (2006)<br /> "[[Biological units and their effect upon the properties and prediction of protein-protein interactions]]", <em>J. Mol. Biol., </em><strong>364</strong>, 1118-1129<em>.</em> </li> <li><a class="external" title="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list uids=15749693" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15749693">PSIbase: a database of Protein Structural Interactome map (PSIMAP).</a><span class="urlexpansion"> (<em>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15749693</em>)</span> Gong S, Yoon G, Jang I, Bolser D, Dafas P, Schroeder M, Choi H, Cho Y, Han K, Lee S, Choi H, Lappe M, Holm L, Kim S, Oh D, Bhak J. Bioinformatics. 2005 Mar 3 </li> <li><a class="external" title="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list uids=15613386" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15613386">Architecture of basic building blocks in protein and domain structural interaction networks</a><span class="urlexpansion"> (<em>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15613386</em>)</span>. Moon HS, Bhak J, Lee KH, Lee D.Bioinformatics. 2005 Apr 15;21(8):1479-86. Epub 2004 Dec 21. </li> <li><a class="external" title="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list uids=15231539" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15231539">Using convex hulls to extract interaction interfaces from known structures.</a><span class="urlexpansion"> (<em>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15231539</em>)</span> Panos Dafas, Dan Bolser, Jacek Gomoluch, Jong Park and Michael Schroeder, Bioinformatics. 10 July 2004. 20(10):1486-1490. </li> <li><a class="external" title="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list uids=15117749" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15117749">HPID: The Human Protein Interaction Database.</a><span class="urlexpansion"> (<em>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15117749</em>)</span> Kyungsook Han, Byungkyu Park, Hyongguen Kim, Jinsun Hong and Jong Park, Bioinformatics, 29 Apr. 2004 (In press) </li> <li><a class="external" title="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list uids=14764552" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14764552">Large scale co-evolution analysis of Protein Structural Interlogues using the global Protein Structural Interactome Map(PSIMAP).</a><span class="urlexpansion"> (<em>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14764552</em>)</span> Wankyu Kim, Dan M. Bolser and Jong Park, Bioinformatics, 2004, 20(7):1138-1150. </li> <li><a class="external" title="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list uids=14531933" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14531933">Visualisation and Graph-theoretic Analysis of a Large-scale Protein Structural Interactome.</a><span class="urlexpansion"> (<em>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14531933</em>)</span> Dan M Bolser, Panos Dafas, Richard Harrington, Jong Park and Michael Schroeder, BMC Bioinformatics, 8 October 2003, 4;45:1471-2105. </li> <li><a class="external" title="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list uids=12538268" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12538268">Visualization and Analysis of Protein Interactions.</a><span class="urlexpansion"> (<em>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12538268</em>)</span> Byonghyon Ju, ByungkyuPark, Jong Park and Kyungsook Han, Bioinformatics, 2003, 19:317-318. </li> <li>Predicting Protein Interactions in Human by Homologous Interactions in Yeast. Hyongguen Kim, Jong Park and Kyungsook Han, Lecture Notes in Computer Science, 2003, 2637:159-165. </li> <li><a class="external" title="http://networkbiology.net" rel="nofollow" href="http://networkbiology.net/">Network Biology</a><span class="urlexpansion"> (<em>http://networkbiology.net</em>)</span>: Datamining Biological Networks. <a class="external" title="http://csdl.computer.org/comp/mags/ex/2002/03/x3toc.htm" rel="nofollow" href="http://csdl.computer.org/comp/mags/ex/2002/03/x3toc.htm">IEEE Intelligent Systems</a><span class="urlexpansion"> (<em>http://csdl.computer.org/comp/mags/ex/2002/03/x3toc.htm</em>)</span>, May/June (Vol. 17, No. 3, pp66-80). 2002 </li> <li><a class="external" title="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list uids=11791232&dopt=Abstract" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11791232&dopt=Abstract">The Conservation of Protein Interaction Network in Evolution.</a><span class="urlexpansion"> (<em>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11791232&dopt=Abstract</em>)</span> <a class="external" title="http://www.jsbi.org/journal/GIW01/GIW01F14.html" rel="nofollow" href="http://www.jsbi.org/journal/GIW01/GIW01F14.html">GIW2001</a><span class="urlexpansion"> (<em>http://www.jsbi.org/journal/GIW01/GIW01F14.html</em>)</span>: The Twelfth International Conference on Genome Informatics, Tokyo Japan, 2001. </li> <li><a class="external" title="http://bio.cc/PSIMAP/Paper/PSIMAP bioinformatics 2001.html" rel="nofollow" href="http://bio.cc/PSIMAP/Paper/PSIMAP_bioinformatics_2001.html">Generating protein interactioin map from incomplete data: application of fold assignment.</a><span class="urlexpansion"> (<em>http://bio.cc/PSIMAP/Paper/PSIMAP_bioinformatics_2001.html</em>)</span> Lappe M, Park J, Niggemann O, Holm L. Bioinformatics. 2001;17 Suppl 1:S149-56. <a class="external" title="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list uids=11473004&dopt=Abstract" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11473004&dopt=Abstract">PMID: 11473004</a><span class="urlexpansion"> (<em>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11473004&dopt=Abstract</em>)</span> [PubMed - indexed for MEDLINE]. <a class="external" title="http://bio.cc/PSIMAP/Paper/bioinformatics paper for fold assignment 2001.pdf" rel="nofollow" href="http://bio.cc/PSIMAP/Paper/bioinformatics_paper_for_fold_assignment_2001.pdf">PDF file</a><span class="urlexpansion"> (<em>http://bio.cc/PSIMAP/Paper/bioinformatics_paper_for_fold_assignment_2001.pdf</em>)</span> </li> <li>Mapping Protein Family Interactions: Intramolecular and Intermolecular Protein Family Interaction Repertoires in the PDB and Yeast , Jong Park, Michael Lappe & Sarah A. Teichmann, Journal of Molecular Biology (2001). <a class="external" title="http://bio.cc/Publish/Paper/JMB published PSIMAP.pdf" rel="nofollow" href="http://bio.cc/Publish/Paper/JMB_published_PSIMAP.pdf">PDF file</a><span class="urlexpansion"> (<em>http://bio.cc/Publish/Paper/JMB_published_PSIMAP.pdf</em>)</span> </li> </ol> <div class="editsection" style="FLOAT: right; MARGIN-LEFT: 5px">[<a title="PSIMAP" href="http://bio.cc/PSIMAP/Mediawiki/index.php?title=PSIMAP&action=edit&section=4">edit</a>]</div> <h2>PSIMAP People </h2> <ul> <li>People who have been involved in PSIMAP in various ways. It is an <strong>open & free</strong> collaboration of people. <ul> <li><strong>Any of you!</strong> Please email us if you want to contribute and want to participate in this research and writing papers with us. </li> </ul> </li> </ul> <ul> <li>Authors: <a title="PSIMAP author and contribution list" href="http://psimap.org/index.php/PSIMAP_author_and_contribution_list">PSIMAP author and contribution list</a> page </li> </ul> <div class="editsection" style="FLOAT: right; MARGIN-LEFT: 5px">[<a title="PSIMAP" href="http://bio.cc/PSIMAP/Mediawiki/index.php?title=PSIMAP&action=edit&section=5">edit</a>]</div> <h2>Major Directory </h2> <p>MIPS_vs_SISF -> the working dir. Paper -> for paper /DB/PDB/PDB100 </p> <p><br /> </p> <div class="editsection" style="FLOAT: right; MARGIN-LEFT: 5px">[<a title="PSIMAP" href="http://bio.cc/PSIMAP/Mediawiki/index.php?title=PSIMAP&action=edit&section=6">edit</a>]</div> <h2>Important files </h2> <ul> <li>(1) Making the first interaction list. make_scop_domain_interaction_pair_table.pl result_pair_skip.psdip (THE output) <ul> <li>Whole chain - chain (upon Sarah's request) </li> <li>Whole chain - Motif (fragment) </li> <li>Motif - Motif </li> </ul> </li> <li>dir.dom.scop.txt_1.48 </li> </ul> <p><br /> </p> <div class="editsection" style="FLOAT: right; MARGIN-LEFT: 5px">[<a title="PSIMAP" href="http://bio.cc/PSIMAP/Mediawiki/index.php?title=PSIMAP&action=edit&section=7">edit</a>]</div> <h2>Data files </h2> <ol> <li>result_pair_skip.psdip.gz /DB/PDB/PDB100 <br /> </li> <li>result_pair_skip_chain_domain.psdip.gz <br /> </li> <li>result_pair_skip_chain_motif_domain.psdip.gz <br /> </li> <li>result_pair_skip_combined_motif_domain.psdip.gz <br /> </li> <li>result_pair_skip_motif_domain.psdip.gz <br /> </li> <li><a class="external" title="http://bio.cc/PSIMAP/consistent expression cluster.txt" rel="nofollow" href="http://bio.cc/PSIMAP/consistent_expression_cluster.txt">consistent_expression_cluster.txt</a><span class="urlexpansion"> (<em>http://bio.cc/PSIMAP/consistent_expression_cluster.txt</em>)</span> (from Sonia) <br /> </li> <li>versatility_summary_100_sorted_comma.piver <br /> </li> </ol> <div class="editsection" style="FLOAT: right; MARGIN-LEFT: 5px">[<a title="PSIMAP" href="http://bio.cc/PSIMAP/Mediawiki/index.php?title=PSIMAP&action=edit&section=8">edit</a>]</div> <h2>Services </h2> <ol> <li>PSIbase <a class="external" title="http://psibase.kaist.ac.kr" rel="nofollow" href="http://psibase.kobic.re.kr"><font color="#800080">server</font></a><span class="urlexpansion"> (<em><a href="http://psibase.kobic.re.kr">http://psibase.kobic.re.kr</a></em>)</span> <br /> </li> </ol> <p><br /> </p> <div class="editsection" style="FLOAT: right; MARGIN-LEFT: 5px">[<a title="PSIMAP" href="http://bio.cc/PSIMAP/Mediawiki/index.php?title=PSIMAP&action=edit&section=9">edit</a>]</div> <h2>File Extensions </h2> <ol> <li>PSDIP : protein structural domain interaction pair <br /> </li> <li>PIVER : Protein Interaction Versatility <br /> </li> </ol> <p><br /> </p> <div class="editsection" style="FLOAT: right; MARGIN-LEFT: 5px">[<a title="PSIMAP" href="http://bio.cc/PSIMAP/Mediawiki/index.php?title=PSIMAP&action=edit&section=10">edit</a>]</div> <h2>BiO Interact Refer , FAQs, Papers </h2> <ol> <li><a class="external" title="http://bio.cc/PSIMAP/Paper/" rel="nofollow" href="http://bio.cc/PSIMAP/Paper/">Paper</a><span class="urlexpansion"> (<em>http://bio.cc/PSIMAP/Paper/</em>)</span>: (/Paper/PSIFA_paper.html) <br /> <ol> <li>Paper/comp_bio_str_inter_map.html </li> <li>Paper/SCOP domain interaction table </li> <li>Word Doc file (edited in VMWARE) </li> </ol> </li> <li>References for interaction studies <br /> </li> </ol> <p><br /> </p> <div class="editsection" style="FLOAT: right; MARGIN-LEFT: 5px">[<a title="PSIMAP" href="http://bio.cc/PSIMAP/Mediawiki/index.php?title=PSIMAP&action=edit&section=11">edit</a>]</div> <h2>Related Research </h2> <ul> <li><a title="Co-evolution study using PSIMAP" href="http://psimap.org/index.php/Co-evolution_study_using_PSIMAP">Co-evolution study using PSIMAP</a> </li> <li>The development of the BIT project </li> </ul> <p><br /> </p> <div class="editsection" style="FLOAT: right; MARGIN-LEFT: 5px">[<a title="PSIMAP" href="http://bio.cc/PSIMAP/Mediawiki/index.php?title=PSIMAP&action=edit&section=12">edit</a>]</div> <h2>Misc </h2> <ul> <li><a class="external" title="http://starryskies.com/articles/spec/hooke.html" rel="nofollow" href="http://starryskies.com/articles/spec/hooke.html"><font color="#800080">Robert Hooke's life</font></a><span class="urlexpansion"> (<em>http://starryskies.com/articles/spec/hooke.html</em>)</span> </li> <li><a class="external" title="http://pqs.ebi.ac.uk/" rel="nofollow" href="http://pqs.ebi.ac.uk/">PQS server in EBI</a><span class="urlexpansion"> (<em>http://pqs.ebi.ac.uk/</em>)</span> (<a class="external" title="http://pqs.ebi.ac.uk/pqs-doc/pqs-doc.shtml" rel="nofollow" href="http://pqs.ebi.ac.uk/pqs-doc/pqs-doc.shtml">background Info of it</a><span class="urlexpansion"> (<em>http://pqs.ebi.ac.uk/pqs-doc/pqs-doc.shtml</em>)</span>) </li> <li>Loredana's paper on interaction <br /> </li> </ul> <hr /> <p>Contact: Jong Bhak, j@bio.cc, jong@kribb.re.kr, Sungsam Gong, ssgong@bio.cc<br /> </p> <p><br /> </p>
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