PCFamily: a web server for searching homologous protein complexes.
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.
Lo
Yu-Shu
YS
Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology and Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan.
Lin
Chun-Yu
CY
Yang
Jinn-Moon
JM
D004921:Erythropoietin / Q000737:chemistry; D020407:Internet; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000235:genetics; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D017467:Receptors, Erythropoietin / Q000737:chemistry; D044786:S-Phase Kinase-Associated Proteins / Q000737:chemistry; D020539:Sequence Analysis, Protein; D012984:Software; D040681:Structural Homology, Protein; D014584:User-Computer Interface
D046912:Multiprotein Complexes; D017467:Receptors, Erythropoietin; D044786:S-Phase Kinase-Associated Proteins; D004921:Erythropoietin