MODBASE: a database of annotated comparative protein structure models and associated resources
| Autor: | Ursula, Pieper, Narayanan, Eswar, Fred P, Davis, Hannes, Braberg, M S, Madhusudhan, Andrea, Rossi, Marc, Marti-Renom, Rachel, Karchin, Ben M, Webb, David, Eramian, Min-Yi, Shen, Libusha, Kelly, Francisco, Melo, Andrej, Sali |
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| Rok vydání: | 2005 |
| Předmět: |
Models
Molecular 0303 health sciences Internet Binding Sites 030302 biochemistry & molecular biology Proteins Ligands Polymorphism Single Nucleotide Article Protein Structure Tertiary Systems Integration 03 medical and health sciences User-Computer Interface Structural Homology Protein Genetics Humans Databases Protein Software 030304 developmental biology |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 |
| Popis: | MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, and improvements in the software for calculating the models. MODBASE currently contains 3 094 524 reliable models for domains in 1 094 750 out of 1 817 889 unique protein sequences in the UniProt database (July 5, 2005); only models based on statistically significant alignments and models assessed to have the correct fold despite insignificant alignments are included. MODBASE also allows users to generate comparative models for proteins of interest with the automated modeling server MODWEB (http://salilab.org/modweb). Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, http://salilab.org/dbali), structurally defined ligand binding sites and structurally defined binary domain interfaces (PIBASE, http://salilab.org/pibase) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, http://salilab.org/LS-SNP). |
| Databáze: | OpenAIRE |
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