The SuMo server: 3D search for protein functional sites
| Autor: | Christophe Combet, François Delfaud, Martin Jambon, Olivier Andrieu, Christophe Geourjon, Gilbert Deléage |
|---|---|
| Přispěvatelé: | Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS) |
| Jazyk: | angličtina |
| Rok vydání: | 2005 |
| Předmět: |
Protein Conformation
Computer science MESH: Sequence Analysis Protein Protein Data Bank (RCSB PDB) MESH: Amino Acid Sequence computer.software_genre 01 natural sciences Biochemistry User-Computer Interface Protein structure MESH: Structure-Activity Relationship MESH: Protein Conformation Sequence Analysis Protein Protein methods Protein Interaction Mapping MESH: Proteins Peptide sequence chemistry.chemical_classification 0303 health sciences Heuristic computer.file_format Ligand (biochemistry) Computer Science Applications Amino acid Computational Mathematics MESH: Internet Computational Theory and Mathematics The Internet Data mining Protein Binding Macromolecule Statistics and Probability Web server Sequence analysis Molecular Sequence Data Computational biology MESH: Imaging Three-Dimensional Structure-Activity Relationship 03 medical and health sciences MESH: Software Imaging Three-Dimensional Structure–activity relationship MESH: Protein Binding [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology Amino Acid Sequence Binding site Molecular Biology 030304 developmental biology MESH: User-Computer Interface Internet Binding Sites MESH: Molecular Sequence Data business.industry MESH: Protein Interaction Mapping Proteins Protein Data Bank 0104 chemical sciences 010404 medicinal & biomolecular chemistry chemistry MESH: Binding Sites business computer Software |
| Zdroj: | Bioinformatics Bioinformatics, Oxford University Press (OUP), 2005, 21 (20), pp.3929-30. ⟨10.1093/bioinformatics/bti645⟩ |
| ISSN: | 1367-4803 1367-4811 |
| DOI: | 10.1093/bioinformatics/bti645⟩ |
| Popis: | International audience; SUMMARY: We provide the scientific community with a web server which gives access to SuMo, a bioinformatic system for finding similarities in arbitrary 3D structures or substructures of proteins. SuMo is based on a unique representation of macromolecules using selected triplets of chemical groups having their own geometry and symmetry, regardless of the restrictive notions of main chain and lateral chains of amino acids. The heuristic for extracting similar sites was used to drive two major large-scale approaches. First, searching for ligand binding sites onto a query structure has been made possible by comparing the structure against each of the ligand binding sites found in the Protein Data Bank (PDB). Second, the reciprocal process, i.e. searching for a given 3D site of interest among the structures of the PDB is also possible and helps detect cross-reacting targets in drug design projects. AVAILABILITY: The web server is freely accessible to academia through http://sumo-pbil.ibcp.fr and full support is available from MEDIT (http://www.medit.fr). CONTACT: mjambon@burnham.org. |
| Databáze: | OpenAIRE |
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