4.8 Article

MODBASE, a database of annotated comparative protein structure models, and associated resources

期刊

NUCLEIC ACIDS RESEARCH
卷 32, 期 -, 页码 D217-D222

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OXFORD UNIV PRESS
DOI: 10.1093/nar/gkh095

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资金

  1. NCI NIH HHS [R33 CA84699] Funding Source: Medline
  2. NCRR NIH HHS [P41 RR01081, P41 RR001081] Funding Source: Medline
  3. NIGMS NIH HHS [P50 GM62529, R01 GM 54762, R01 GM054762, P50 GM062529] Funding Source: Medline
  4. NATIONAL CANCER INSTITUTE [R33CA084699] Funding Source: NIH RePORTER
  5. NATIONAL CENTER FOR RESEARCH RESOURCES [P41RR001081] Funding Source: NIH RePORTER
  6. NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [P50GM062529, R01GM054762] Funding Source: NIH RePORTER

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MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on. the MODELLER package for fold assignment, sequence-structure alignment, model building and model assessment (http:/saillab.org/modeller). MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different data sets. The largest data set contains 1 262 629 models for domains in 659 495 out of 1182126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included. Another model data set supports target selection and structure-based annotation by the New York Structural Genomics Research Consortium; e.g. the 53 new structures produced by the consortium allowed us to characterize structurally 24113 sequences. MODBASE also contains binding site predictions for small ligands and a set of predicted interactions between pairs of modeled sequences from the same genome. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments (DBALI, http://salilab.org/dbali) as well as web servers for automated comparative modeling with MODPIPE (MODWEB, http://salilab. org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb).

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