دورية أكاديمية
A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0].
| العنوان: | A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0]. |
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| المؤلفون: | Bogetti AT; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA., Mostofian B; Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR., Dickson A; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI., Pratt AJ; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA., Saglam AS; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA., Harrison PO; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA., Adelman JL; Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA; currently unaffiliated., Dudek M; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA., Torrillo PA; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA., DeGrave AJ; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA.; Current address: Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA., Adhikari U; Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR.; Current address: Department of Chemistry, Missouri Valley College, Marshall, MO., Zwier MC; Department of Chemistry, Drake University, Des Moines, IA., Zuckerman DM; Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR., Chong LT; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA. |
| المصدر: | Living journal of computational molecular science [Living J Comput Mol Sci] 2019; Vol. 1 (2). Date of Electronic Publication: 2019 Oct 04. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: University of Colorado Boulder Country of Publication: United States NLM ID: 101736625 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2575-6524 (Electronic) NLM ISO Abbreviation: Living J Comput Mol Sci Subsets: PubMed not MEDLINE |
| أسماء مطبوعة: | Original Publication: Boulder, CO : University of Colorado Boulder |
| مستخلص: | The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in generating pathways and rate constants for rare events such as protein folding and protein binding using atomistic molecular dynamics simulations. Here we present five tutorials instructing users in the best practices for preparing, carrying out, and analyzing WE simulations for various applications using the WESTPA software. Users are expected to already have significant experience with running standard molecular dynamics simulations using the underlying dynamics engine of interest (e.g. Amber, Gromacs, OpenMM). The tutorials range from a molecular association process in explicit solvent to more complex processes such as host-guest association, peptide conformational sampling, and protein folding. Competing Interests: 9Potentially Conflicting Interests The authors declare no conflicting interests. |
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| معلومات مُعتمدة: | R01 GM115805 United States GM NIGMS NIH HHS; R01 GM111805 United States GM NIGMS NIH HHS; R01 GM115762 United States GM NIGMS NIH HHS; T32 DK061296 United States DK NIDDK NIH HHS; R01 GM130794 United States GM NIGMS NIH HHS; T32 GM007266 United States GM NIGMS NIH HHS; R01 GM115185 United States GM NIGMS NIH HHS |
| تواريخ الأحداث: | Date Created: 20200513 Latest Revision: 20201009 |
| رمز التحديث: | 20221213 |
| مُعرف محوري في PubMed: | PMC7213600 |
| DOI: | 10.33011/livecoms.1.2.10607 |
| PMID: | 32395705 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 2575-6524 |
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| DOI: | 10.33011/livecoms.1.2.10607 |