3D-partner: a web server to infer interacting partners and binding models
| Autor: | Yung Chiang Chen, Wen Chang Hsu, Yu Shu Lo, Jinn-Moon Yang |
|---|---|
| Rok vydání: | 2007 |
| Předmět: |
Web server
Saccharomyces cerevisiae Proteins Molecular Sequence Data Saccharomyces cerevisiae Computational biology Biology Bioinformatics computer.software_genre User-Computer Interface Protein sequencing Similarity (network science) Sequence Analysis Protein Protein Interaction Mapping Computer Graphics Genetics Amino Acid Sequence Binding site Databases Protein Peptide sequence Sequence Binding Sites Sequence Homology Amino Acid Gene Expression Profiling Proteins Articles Function (mathematics) Protein Structure Tertiary Template computer Protein Binding |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkm346 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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