ArticleJournal of structural and functional genomics2016
HOMCOS: an updated server to search and model complex 3D structures.
Article in Journal of structural and functional genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 45 citations in OpenAlex.
- Evolutionary and Functional Insights of Leucine-Rich Alpha-2-Glycoprotein 1 in Cetacean Wound Healing: The First Identification of LRG1 in the Bottlenose Dolphin (Tursiops truncatus).Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Article
- Assessing Structural Classification Using AlphaFold2 Models Through ECOD-Based Comparative Analysis.Proteins · 2025Article
- Protein Data Bank Japan: Computational Resources for Analysis of Protein Structures.Journal of molecular biology · 2025Article
- Protein Data Bank Japan: Improved tools for sequence-oriented analysis of protein structures.Protein science : a publication of the Protein Society · 2025Article
- PPI3D: a web server for searching, analyzing and modeling protein-protein, protein-peptide and protein-nucleic acid interactions.Nucleic acids research · 2024Article
- The Potential Role of the Leucocyte Immunoglobulin-Like Receptors in Kidney Transplant Rejection: A Mini Review.Transplant international : official journal of the European Society for Organ Transplantation · 2024Review
- Identification of ultra-rare disruptive variants in voltage-gated calcium channel-encoding genes in Japanese samples of schizophrenia and autism spectrum disorder.Translational psychiatry · 2022Article
- Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data.Protein science : a publication of the Protein Society · 2022Article
- Recent advances in user-friendly computational tools to engineer protein function.Briefings in bioinformatics · 2021Review
- Adaptation of the endemic coronaviruses HCoV-OC43 and HCoV-229E to the human host.Virus evolution · 2021Article
- Functional characterization of rare NRXN1 variants identified in autism spectrum disorders and schizophrenia.Journal of neurodevelopmental disorders · 2020Article
- Detection of cave pockets in large molecules: Spaces into which internal probes can enter, but external probes from outside cannot.Biophysics and physicobiology · 2019Article
- InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs.Nucleic acids research · 2018Article
- Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state.Nucleic acids research · 2018Article
- Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.Molecules (Basel, Switzerland) · 2017Article
- A novel rare variant R292H in RTN4R affects growth cone formation and possibly contributes to schizophrenia susceptibility.Translational psychiatry · 2017Article
- Rare genetic variants in CX3CR1 and their contribution to the increased risk of schizophrenia and autism spectrum disorders.Translational psychiatry · 2017Article
- Multimer recognition and secretion by the non-classical secretion pathway in Bacillus subtilis.Scientific reports · 2017Article
- Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.Nucleic acids research · 2017Article
- VaProS: a database-integration approach for protein/genome information retrieval.Journal of structural and functional genomics · 2016Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The HOMCOS server ( http://homcos.pdbj.org ) was updated for both searching and modeling the 3D complexes for all molecules in the PDB. As compared to the previous HOMCOS server, the current server targets all of the molecules in the PDB including proteins, nucleic acids, small compounds and metal ions. Their binding relationships are stored in the database. Five services are available for users. For the services "Modeling a Homo Protein Multimer" and "Modeling a Hetero Protein Multimer", a user can input one or two proteins as the queries, while for the service "Protein-Compound Complex", a user can input one chemical compound and one protein. The server searches similar molecules by BLAST and KCOMBU. Based on each similar complex found, a simple sequence-replaced model is quickly generated by replacing the residue names and numbers with those of the query protein. A target compound is flexibly superimposed onto the template compound using the program fkcombu. If monomeric 3D structures are input as the query, then template-based docking can be performed. For the service "Searching Contact Molecules for a Query Protein", a user inputs one protein sequence as the query, and then the server searches for its homologous proteins in PDB and summarizes their contacting molecules as the predicted contacting molecules. The results are summarized in "Summary Bars" or "Site Table"display. The latter shows the results as a one-site-one-row table, which is useful for annotating the effects of mutations. The service "Searching Contact Molecules for a Query Compound" is also available.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.