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<HTML> <HEAD> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <TITLE>[pdbjlvh2]HOMCOS : Searching and Modeling of 3D Structures of Complexes</TITLE> </HEAD> <BODY BGCOLOR="#FFFFFF" LINK="#202070" VLINK="#202070"> <CENTER> <IMG SRC="https://homcos.pdbj.org/IMG/homcos_large.png"> <H4>HOMCOS : Searching and Modeling of 3D Structures of Complexes</H4> </CENTER> <TABLE BORDER="0"> <TR> <TD> <A HREF="https://homcos.pdbj.org/cgi-bin/index.cgi?LANG=ja">[Go to Japanese page]</A> </TD> <TD> <A HREF="https://homcos.pdbj.org/cgi-bin/help_homcos.cgi?LANG=en&service=all"><IMG SRC="https://homcos.pdbj.org/IMG/help.png" ALIGN="middle">Help page</A> </TD> </TR> </TABLE> <HR> HOMCOS(<U>HOM</U>ology modeling of <U>CO</U>mplex <U>S</U>tructure) is a server for modeling complex 3D structures using 3D molecular similarities based on template complex 3D structures in PDB. For a given amino acid sequence or a chemical strucvure, the server provides list of contacting molecules in PDB, predicted complex 3D structure based on the template PDB structures. <A HREF="http://blast.ncbi.nlm.nih.gov" TARGET=_BLANK">BLAST</A> is employed for the amino acids sequence search, <A HREF="https://pdbj.org/kcombu" TARGET=_BLANK>KCOMBU</A> is used for the chemical structure search.<BR> <CENTER> <HR> <TABLE BORDER="1"> <TR BGCOLOR="#F0F0F0"> <TD COLSPAN="2">Services</TD> <TD>Queries</TD> <TD>Descriptions</TD> </TR> <TR> <TD ROWSPAN="2" BGCOLOR="#FFFFFF"><B>Searching Contact Molecules</B></TD> <TD NOWRAP><A HREF="https://homcos.pdbj.org/cgi-bin/prot_sch_inp.cgi?&LANG=en"><IMG SRC="https://homcos.pdbj.org/IMG/prot_sch_small.png" BORDER="0" ALIGN="middle"><B>Searching Contact Molecules for Query Protein</B></A></TD> <TD>Sequence</TD> <TD>Search contact molecules with similar proteins to a given query sequence</TD> </TR> <TR> <TD NOWRAP><A HREF="https://homcos.pdbj.org/cgi-bin/comp_sch_inp.cgi?&LANG=en"><IMG SRC="https://homcos.pdbj.org/IMG/comp_sch_small.png" BORDER="0" ALIGN="middle"><B>Searching Contact Proteins for Query Compound</B> <TD>Compound</TD> <TD>Search contact proteins with similar compounds to a given query compounds</TD> </TR> <TR> <TD ROWSPAN="3" BGCOLOR="#FFFFFF"><B>Modeling Complex 3D Structure</B></TD> <TD NOWRAP><A HREF="https://homcos.pdbj.org/cgi-bin/homo_model_inp.cgi?&LANG=en"><IMG SRC="https://homcos.pdbj.org/IMG/homo_model_small.png" BORDER="0" ALIGN="middle"><B>Homo Protein Multimer</B></A></TD> <TD>Sequence</TD> <TD>Model 3D structure of homo-multimer for one given sequence using homology-modeling technique.</TD> </TR> <TR> <TD NOWRAP><A HREF="https://homcos.pdbj.org/cgi-bin/hetero_model_inp.cgi?&LANG=en"><IMG SRC="https://homcos.pdbj.org/IMG/hetero_model_small.png" BORDER="0" ALIGN="middle"><B>Hetero Protein Multimer</B></A></TD> <TD>Two Sequences</TD> <TD>Model 3D structure of hetero-multimer for two given sequence using homology-modeling technique.</TD> </TR> <TR> <TD NOWRAP><A HREF="https://homcos.pdbj.org/cgi-bin/procomp_model_inp.cgi?&LANG=en"><IMG SRC="https://homcos.pdbj.org/IMG/procomp_model_small.png" BORDER="0" ALIGN="middle"><B>Protein-Compound Complex</B></A></TD> <TD>Sequence and Compound</TD> <TD>Model 3D structure of protein-compound complex for one given sequence and one given chemical structure using homology-modeling technique.</TD> </TR> </TABLE> </CENTER> <A HREF="https://homcos.pdbj.org/cgi-bin/download_data.cgi?LANG=en">[Download HOMCOS data]</A>: <I>Release of <A HREF="http://pdbj.org" TARGET=_BLANK>PDB</I>:20250305</A>, <I>Release of <A HREF="https://www.uniprot.org/" TARGET=_BLANK>UniProt</I>:2025_01</A> <I>Release of <A HREF="https://www.genome.jp/kegg" TARGET=_BLANK>KEGG</I>:2022-03-07</A> <A HREF="https://homcos.pdbj.org/cgi-bin/download_kegg.cgi?LANG=en" TARGET=_BLANK>[3Dfiles of KEGG_COMPOUND and DRUG]</A> <HR> <CENTER><H4><IMG SRC="https://homcos.pdbj.org/IMG_SARS_COV_2/coronavirus_feature-page.png" WIDTH=60 ALIGN="MIDDLE">We open the page for proteins and compounds related to Coronavirus SARS-CoV-2!(PDB_UPDATE:20250305)<BR>https://homcos.pdbj.org/cgi-bin/sars_cov_2.cgi?LANG=en</A></H4></CENTER> <CENTER><H4><A HREF="https://homcos.pdbj.org/cgi-bin/3Dcluster.cgi?LANG=en">Analysis of mutation of 3D clusters with the help of HOMCOS</A></H4></CENTER> <CENTER><H4>TOGOTV releases <A HREF="https://togotv.dbcls.jp/20220618.html" TARGET=_BLANK>a Japanese tutorial movie for HOMCOS (https://togotv.dbcls.jp/20220618.html) </A>(2022/06/17)</H4></CENTER> <HR> <A HREF="http://blast.ncbi.nlm.nih.gov" TARGET=_BLANK">BLAST</A> is employed for the amino acids sequence search, <A HREF="https://pdbj.org/kcombu" TARGET=_BLANK>KCOMBU</A> is used for the chemical structure search.<P> HOMCOS is developed and maintained by <A HREF="http://www.protein.osaka-u.ac.jp/rcsfp/databases/index.html.en" TARGET=_BLANK>Protein Data Bank Japan, IPR, Osaka University</A>. It is now supported by the project <A HREF="http://pford.jp/p4d/ipc1/" TARGET=_BLANK>"Platform for Drug Discovery, Informatics, and Structural Life Science"</A> by MEXT, Japan.<P> This server is based on the concept of <A HREF="http://nar.oxfordjournals.org/content/36/suppl_2/W185.full" TARGET=_BLANK>HOMCOS server</A> developed by NAIST.<P> A part of the services of the HOMCOS server can be accessed by <A HREF="http://pford.info/vapros" TARGET=_BLANK>VaProS server</A>. HOMCOS is called "3D Interaction" in the VaProS server.<P> <B>References</B><BR> <UL> <LI>Kawabata T. (2016) HOMCOS: an update server to search and model complex 3D structures. <I>J.Struct.Funct.Genomics</I>. <B>17</B>,83-99. <A HREF="http://www.ncbi.nlm.nih.gov/pubmed/27522608" TARGET=_BLANK>[PubMed]</A> <A HREF="http://link.springer.com/article/10.1007/s10969-016-9208-y?wt_mc=Internal.Event.1.SEM.ArticleAuthorOnlineFirst" TARGET=_BLANK>[Publisher]</A> <LI>Fukuhara N., Kawabata T. (2008) HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures. <I>Nucleic Acids Res.</I>, <B>36</B>, W185-W189. <A HREF="http://www.ncbi.nlm.nih.gov/pubmed/18442990" TARGET=_BLANK>[PubMed]</A> </UL> Comments and Questions to:<IMG SRC="https://homcos.pdbj.org/IMG/email_kawabata.png" align="middle" height=30> </BODY> </HTML>