Abstract:
:As protein-protein interactions are crucial in most biological processes, it is valuable to understand how and where protein pairs interact. We developed a web server HOMCOS (Homology Modeling of Complex Structure, http://biunit.naist.jp/homcos) to predict interacting protein pairs and interacting sites by homology modeling of complex structures. Our server is capable of three services. The first is modeling heterodimers from two query amino acid sequences posted by users. The server performs BLAST searches to identify homologous templates in the latest representative dataset of heterodimer structures generated from the PQS database. Structure validity is evaluated by the combination of sequence similarity and knowledge-based contact potential energy as previously described. The server generates a sequence-replaced model PDB file and a MODELLER script to build full atomic models of complex structures. The second service is modeling homodimers from one query sequence. The third service is identification of potentially interacting proteins for one query sequence. The server searches the dataset of heterodimer structures for a homologous template, outputs the candidate interacting sequences in the Uniprot database homologous for the interacting partner template proteins. These features are useful for wide range of researchers to predict putative interaction sites and interacting proteins.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Fukuhara N,Kawabata Tdoi
10.1093/nar/gkn218subject
Has Abstractpub_date
2008-07-01 00:00:00pages
W185-9issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkn218journal_volume
36pub_type
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