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- Title
CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins.
- Authors
Turcan, Alistair; Zivkovic, Anna; Thompson, Dylan; Wong, Lorraine; Johnson, Lauren; Jagodzinski, Filip
- Abstract
Elucidating protein rigidity offers insights about protein conformational changes. An understanding of protein motion can help speed drug development, and provide general insights into the dynamic behaviors of biomolecules. Existing rigidity analysis techniques employ fine-grained, all-atom modeling, which has a costly run-time, particularly for proteins made up of more than 500 residues. In this work, we introduce coarse-grained rigidity analysis, and showcase that it provides flexibility information about a protein that is similar in accuracy to an all-atom modeling approach. We assess the accuracy of the coarse-grained method relative to an all-atom approach via a comparison metric that reasons about the largest rigid clusters of the two methods. The apparent symmetry between the all-atom and coarse-grained methods yields very similar results, but the coarse-grained method routinely exhibits 40% reduced run-times. The CGRAP web server outputs rigid cluster information, and provides data visualization capabilities, including a interactive protein visualizer.
- Subjects
INTERNET servers; PROTEIN analysis; DRUG development; BIOMOLECULES; DATA visualization
- Publication
Symmetry (20738994), 2021, Vol 13, Issue 12, p2401
- ISSN
2073-8994
- Publication type
Article
- DOI
10.3390/sym13122401