ArticleNucleic acids research2008
HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Statistical analysis of sequential motifs at biologically relevant protein-protein interfaces.Computational and structural biotechnology journal · 2024Article
- Struct2Graph: a graph attention network for structure based predictions of protein-protein interactions.BMC bioinformatics · 2022Article
- Protein-protein interaction prediction with deep learning: A comprehensive review.Computational and structural biotechnology journal · 2022Review
- A single amino acid polymorphism in a conserved effector of the multihost blast fungus pathogen expands host-target binding spectrum.PLoS pathogens · 2021Article
- Network-based protein-protein interaction prediction method maps perturbations of cancer interactome.PLoS genetics · 2021Article
- Methods for Molecular Modelling of Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Databases for Protein-Protein Interactions.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota.Microbiome · 2020Article
- Machine-learning techniques for the prediction of protein-protein interactions.Journal of biosciences · 2019Article
- ImmtorLig_DB: repertoire of virtually screened small molecules against immune receptors to bolster host immunity.Scientific reports · 2019Article
- Computational Molecular Docking and X-ray Crystallographic Studies of Catechins in New Drug Design Strategies.Molecules (Basel, Switzerland) · 2018Review
- MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.BMC bioinformatics · 2018Article
- Non-interacting proteins may resemble interacting proteins: prevalence and implications.Scientific reports · 2017Article
- HOMCOS: an updated server to search and model complex 3D structures.Journal of structural and functional genomics · 2016Article
- AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana.Plant molecular biology · 2016Article
- In silico predicted structural and functional insights of all missense mutations on 2B domain of K1/K10 causing genodermatoses.Oncotarget · 2016Article
- Altered acetylation and succinylation profiles in Corynebacterium glutamicum in response to conditions inducing glutamate overproduction.MicrobiologyOpen · 2016Article
- Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution.Evolution; international journal of organic evolution · 2015Article
- Lessons in Protein Design from Combined Evolution and Conformational Dynamics.Scientific reports · 2015Article
- (PS)2: protein structure prediction server version 3.0.Nucleic acids research · 2015Article
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2 authors.
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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.
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