ArticleNucleic acids research2007
3D-partner: a web server to infer interacting partners and binding models.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Identification of the HNSC88 Molecular Signature for Predicting Subtypes of Head and Neck Cancer.International journal of molecular sciences · 2023Article
- Membrane protein-regulated networks across human cancers.Nature communications · 2019Article
- A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations.BMC systems biology · 2018Article
- Non-interacting proteins may resemble interacting proteins: prevalence and implications.Scientific reports · 2017Article
- A calmodulin like EF hand protein positively regulates oxalate decarboxylase expression by interacting with E-box elements of the promoter.Scientific reports · 2015Article
- Module organization and variance in protein-protein interaction networks.Scientific reports · 2015Article
- Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping.PloS one · 2015Article
- Structural bioinformatics of the interactome.Annual review of biophysics · 2014Review
- Genome-wide structural modelling of TCR-pMHC interactions.BMC genomics · 2013Article
- Inferring homologous protein-protein interactions through pair position specific scoring matrix.BMC bioinformatics · 2013Article
- MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates.Nucleic acids research · 2012Article
- Computing the protein binding sites.BMC bioinformatics · 2012Article
- Steric recognition of T-cell receptor contact residues is required to map mutant epitopes by immunoinformatical programmes.Immunology · 2012Article
- IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins.Nucleic acids research · 2012Article
- Novel histone H3 binding protein ORF158L from the Singapore grouper iridovirus.Journal of virology · 2011Article
- PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes.Nucleic acids research · 2011Article
- 3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes.BMC genomics · 2010Article
- Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines.BMC bioinformatics · 2010Article
- PCFamily: a web server for searching homologous protein complexes.Nucleic acids research · 2010Article
- Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites.Nucleic acids research · 2010Article
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4 authors.
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Abstract
The 3D-partner is a web tool to predict interacting partners and binding models of a query protein sequence through structure complexes and a new scoring function. 3D-partner first utilizes IMPALA to identify homologous structures (templates) of a query from a heterodimer profile library. The interacting-partner sequence profiles of these templates are then used to search interacting candidates of the query from protein sequence databases (e.g. SwissProt) by PSI-BLAST. We developed a new scoring function, which includes the contact-residue interacting score (e.g. the steric, hydrogen bonds, and electrostatic interactions) and the template consensus score (e.g. couple-conserved residue and the template similarity scores), to evaluate how well the interfaces between the query and interacting candidates. Based on this scoring function, 3D-partner provides the statistic significance, the binding models (e.g. hydrogen bonds and conserved amino acids) and functional annotations of interacting partners. The correlation between experimental energies and predicted binding affinities of our scoring function is 0.91 on 275 mutated residues from the ASEdb. The average precision of the server is 0.72 on 563 queries and the execution time of this server for a query is approximately 15 s on average. These results suggest that the 3D-partner server can be useful in protein-protein interaction predictions and binding model visualizations. The server is available online at: http://3D-partner.life.nctu.edu.tw.
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