CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins
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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-12-01
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| Series: | Symmetry |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-8994/13/12/2401 |
| _version_ | 1797500312726011904 |
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| author | Alistair Turcan Anna Zivkovic Dylan Thompson Lorraine Wong Lauren Johnson Filip Jagodzinski |
| author_facet | Alistair Turcan Anna Zivkovic Dylan Thompson Lorraine Wong Lauren Johnson Filip Jagodzinski |
| author_sort | Alistair Turcan |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T03:00:06Z |
| format | Article |
| id | doaj.art-865a05efa1fa4b94b74ac942b731beb5 |
| institution | Directory Open Access Journal |
| issn | 2073-8994 |
| language | English |
| last_indexed | 2024-03-10T03:00:06Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Symmetry |
| spelling | doaj.art-865a05efa1fa4b94b74ac942b731beb52023-11-23T10:46:40ZengMDPI AGSymmetry2073-89942021-12-011312240110.3390/sym13122401CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of ProteinsAlistair Turcan0Anna Zivkovic1Dylan Thompson2Lorraine Wong3Lauren Johnson4Filip Jagodzinski5Department of Computer Science, Western Washington University, Bellingham, WA 98225, USADepartment of Computer Science, Western Washington University, Bellingham, WA 98225, USADepartment of Computer Science, Western Washington University, Bellingham, WA 98225, USADepartment of Computer Science, Western Washington University, Bellingham, WA 98225, USADepartment of Computer Science, Western Washington University, Bellingham, WA 98225, USADepartment of Computer Science, Western Washington University, Bellingham, WA 98225, USAElucidating 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.https://www.mdpi.com/2073-8994/13/12/2401rigidity analysisbiomoleculesproteinsflexibility |
| spellingShingle | Alistair Turcan Anna Zivkovic Dylan Thompson Lorraine Wong Lauren Johnson Filip Jagodzinski CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins Symmetry rigidity analysis biomolecules proteins flexibility |
| title | CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins |
| title_full | CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins |
| title_fullStr | CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins |
| title_full_unstemmed | CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins |
| title_short | CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins |
| title_sort | cgrap a web server for coarse grained rigidity analysis of proteins |
| topic | rigidity analysis biomolecules proteins flexibility |
| url | https://www.mdpi.com/2073-8994/13/12/2401 |
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