PCFamily: a web server for searching homologous protein complexes

Abstract

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.

Membrane protein-regulated networks across human cancers

“…Based on our previous works 13,14,65–68 , we statistically analyzed and simplified these six scores ranging from 0 to 1 (the total score S SIM ranges from 0 to 6). The detailed scoring method and scheme for identifying MP-interacting protein candidates are as follows.…”

Steric recognition of T‐cell receptor contact residues is required to map mutant epitopes by immunoinformatical programmes

“…We have proposed a template‐based scoring function to determine the reliability of protein–protein interactions 36 and to identify template‐based homologous protein complexes 42 derived from a structural complex. To measure the protein–peptide interaction score, the scoring function is defined as:…”

MoNetFamily: a web server to infer homologous modules and module–module interaction networks in vertebrates

“…For each module candidate, this server provides the neighboring modules and MMIs ( Supplementary Figure S1C ) in MMI networks of H. sapiens , M. musculus and D. rerio ( Figures 1 C and 2 ) through homologous modules. Next, the homologous modules of the template candidate are derived from the PPI families ( 13 , 18 , 19 ) ( Figure 1 B and D). According to homologous modules and PPIs, we statistically calculated MMIs ( Figure 2 D) and MMI networks across multiple species using the hypergeometric distribution.…”

“…Here, the protein aligned ratio ≥ 0.5 and PPI aligned ratio ≥ 0.3 are considered as topology similarity between two modules according to the statistical analysis of 75 706 modules derived from 370 module templates in KEGG MODULE database with 1442 species ( 8 ) ( Supplementary Figure S2 ). For each template in the MoNetFamily server (1975 non-redundant modules), we added its PPIs according to our previous sequence-based homologous PPIs (PPISearch with joint E -value ≤ 10 − 70 ) ( 13 ) and structure-based homologous PPIs (PCFamily with Z -value ≥ 4) ( 19 ) derived from the following PPI databases: (i) 461 077 experimental PPIs in the annotated PPI databases [IntAct ( 20 ), MIPS ( 21 ), DIP ( 22 ), MINT ( 23 ) and BioGRID ( 24 )]; (ii) 9657 PPIs from PDB crystal structures ( 17 ). Please note that our analysis is limited to physical PPIs, specifically protein complexes.…”

“…The MMI can be quantified by the PPIs between two modules ( 2 , 10 ). To determine the MMI between two modules, we added inter-module PPIs through our previous homologous PPIs derived from the six public PPI databases ( 13 , 19 ). Here, we decided the MMI based on the P -value of the hypergeometric distribution ( 10 ) defined as where x is observed annotated inter-module PPIs [e.g.…”