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The SWISS-MODEL Repository-new features and functionality
Stefan Bienert1,2, Andrew Waterhouse1,2, Tjaart A P de Beer1,2
1Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.
Nucleic Acids Research
|December 1, 2016
Summary
The SWISS-MODEL Repository (SMR) now offers over 400,000 3D protein models with enhanced features. This update improves target coverage, model quality, and provides open access to model coordinates for broader research use.
Area of Science:
- Structural Bioinformatics
- Computational Biology
- Protein Modeling
Background:
- The SWISS-MODEL Repository (SMR) is a crucial resource for 3D protein structure models.
- Homology modeling is essential for understanding protein function and structure.
- Existing databases require updates to improve coverage and accessibility.
Purpose of the Study:
- To report recent updates and new features of the SWISS-MODEL Repository.
- To enhance the accessibility and utility of protein structure models.
- To facilitate the reuse of protein models in diverse research applications.
Main Methods:
- Utilized the automated SWISS-MODEL homology modeling pipeline.
- Implemented improvements in target coverage and functional annotations.
- Introduced a new update concept with regular and on-demand model refreshes.
Main Results:
- SMR now contains over 400,000 high-quality protein models, covering 20% of Swiss-Prot/UniProtKB.
- Enhanced in-page visualization and model quality estimates are now available.
- A REST-API and open licensing model enable bulk downloads and model reuse.
Conclusions:
- The updated SWISS-MODEL Repository offers expanded coverage and improved features.
- New access and update mechanisms foster wider adoption and application of protein models.
- SMR continues to be a vital resource for structural biology research.
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