DoSA: Database of Structural Alignments
| Autor: | Alexandre G. de Brevern, Bernard Offmann, Garima Agarwal, Narayanaswamy Srinivasan, Mohammed Iftekhar, Swapnil Mahajan |
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| Přispěvatelé: | Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Molecular Biophysics Unit, Indian Institute of Science, GR-Ex, Laboratoire d'Excellence, GR-Ex, National Centre for Biological Sciences [TIFR] (NCBS), Tata Institute for Fundamental Research (TIFR), Unité de fonctionnalité et ingénierie de protéines (UFIP), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), MBU, Indian Institute of Science-Indian Institute of Science, Indo-French collaborative grant (CEFIPRA/IFCPAR 3903-E) The Ministry of Research (France) The University Paris Diderot, Sorbonne Paris Cite (France) The National Institute of Blood Transfusion (INTS, France) The National Institute of Health and Medical Research (INSERM, France) The Laboratories of Excellence, GR-Ex (France) The University of Nantes (France) Fonds Européen de Dévelopment Régional and Conseil Regional de La Réunion [20100079, Tiers: 144645] Department of Biotechnology (India), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA), de Brevern, Alexandre G. |
| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Models
Molecular PALI substitution matrix optimisation Statistics as Topic MESH: Amino Acid Sequence Molecular Biophysics Unit computer.software_genre Protein structure MESH: Proteins Databases Protein Structural motif database [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM] MESH: Structural Homology Protein 0303 health sciences Protein function [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] Database 030302 biochemistry & molecular biology [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] CLUSTALW Original Article Structural alphabet General Agricultural and Biological Sciences MESH: Models Molecular Information Systems MESH: Databases Protein Molecular Sequence Data Biology iPBA General Biochemistry Genetics and Molecular Biology Substitution matrix Access to Information 03 medical and health sciences [SDV.BBM] Life Sciences [q-bio]/Biochemistry Molecular Biology [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology Amino Acid Sequence protein structure Spatial Orientations MESH: Statistics as Topic 030304 developmental biology MESH: Molecular Sequence Data Proteins Protein superfamily MESH: Access to Information Functional integrity Structural Homology Protein [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] protein structure superimposition computer |
| Zdroj: | Database-The journal of Biological Databases and Curation Database-The journal of Biological Databases and Curation, Oxford University Press, 2013, 2013, pp.bat048. ⟨10.1093/database/bat048⟩ Database-The journal of Biological Databases and Curation, 2013, 2013, pp.bat048. ⟨10.1093/database/bat048⟩ Database: The Journal of Biological Databases and Curation |
| ISSN: | 1758-0463 |
| DOI: | 10.1093/database/bat048⟩ |
| Popis: | International audience; Protein structure alignment is a crucial step in protein structure-function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These regions are not well superimposed because of differences in their spatial orientations. The Database of Structural Alignments (DoSA) addresses this gap in identification of local structural similarities obscured in global protein structural alignments by realigning SVRs using an algorithm based on protein blocks. A set of protein blocks is a structural alphabet that abstracts protein structures into 16 unique local structural motifs. DoSA provides unique information about 159,780 conformationally similar and 56,140 conformationally dissimilar SVRs in 74 705 pairwise structural alignments of homologous proteins. The information provided on conformationally similar and dissimilar SVRs can be helpful to model loop regions. It is also conceivable that conformationally similar SVRs with conserved residues could potentially contribute toward functional integrity of homologues, and hence identifying such SVRs could be helpful in understanding the structural basis of protein function. Database URL: http://bo-protscience.fr/dosa/ |
| Databáze: | OpenAIRE |
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