PCFamily: A web server for searching homologous protein complexes

Yu Shu Lo, Chun-Yu Lin, Jinn-Moon Yang*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


The proteins in a cell often assemble into complexes to carry out their functions and play an essential role of biological processes. The PCFamily server identifies template-based homologous protein complexes [called protein complex family (PCF)] and infers functional modules of the query proteins. This server first finds homologous structure complexes of the query using BLASTP to search the structural template database (11 263 complexes). PCFamily then searches the homologous complexes of the templates (query) from a complete genomic database (Integr8 with 6 352 363 protein sequences in 2274 species). According to these homologous complexes across multiple species, this sever infers binding models (e.g. hydrogen-bonds and conserved amino acids in the interfaces), functional modules, and the conserved interacting domains and Gene Ontology annotations of the PCF. Experimental results demonstrate that the PCFamily server can be useful for binding model visualizations and annotating the query proteins. We believe that the server is able to provide valuable insights for determining functional modules of biological networks across multiple species. The PCFamily sever is available at http://pcfamily.life.nctu.edu.tw.

Original languageEnglish
Article numbergkq464
Pages (from-to)W516–W522
Number of pages7
JournalNucleic Acids Research
Issue numberSUPPL. 2
StatePublished - 1 Jul 2010


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