HOMCOS: an updated server to search and model complex 3D structures.

The HOMCOS server ( http://homcos.pdbj.org ) was updated for both searching and modeling the 3D complexes for all molecules in the PDB. As compared to the previous HOMCOS server, the current server targets all of the molecules in the PDB including proteins, nucleic acids, small compounds and metal ions. Their binding relationships are stored in the database. Five services are available for users. For the services "Modeling a Homo Protein Multimer" and "Modeling a Hetero Protein Multimer", a user can input one or two proteins as the queries, while for the service "Protein-Compound Complex", a user can input one chemical compound and one protein. The server searches similar molecules by BLAST and KCOMBU. Based on each similar complex found, a simple sequence-replaced model is quickly generated by replacing the residue names and numbers with those of the query protein. A target compound is flexibly superimposed onto the template compound using the program fkcombu. If monomeric 3D structures are input as the query, then template-based docking can be performed. For the service "Searching Contact Molecules for a Query Protein", a user inputs one protein sequence as the query, and then the server searches for its homologous proteins in PDB and summarizes their contacting molecules as the predicted contacting molecules. The results are summarized in "Summary Bars" or "Site Table"display. The latter shows the results as a one-site-one-row table, which is useful for annotating the effects of mutations. The service "Searching Contact Molecules for a Query Compound" is also available.