Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 10, Issue 11, Pages 5047-5056Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct500381c
Keywords
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Funding
- National Institutes of Health through NIH Director's New Innovator Award Program [DP2-OD007237]
- NSF XSEDE Supercomputer resources grant [RAC CHE060073N]
- National Science Foundation's Graduate Research Fellowship Program
- Alfred Benzon Foundation
- National Biomedical Computation Resource (NBCR) [P41 GM103426]
- Office of Advanced Cyberinfrastructure (OAC)
- Direct For Computer & Info Scie & Enginr [0910735] Funding Source: National Science Foundation
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Analysis of macromolecular/small-molecule binding pockets can provide important insights into molecular recognition and receptor dynamics. Since its release in 2011, the POVME (POcket Volume MEasurer) algorithm has been widely adopted as a simple-to-use tool for measuring and characterizing pocket volumes and shapes. We here present POVME 2.0, which is an order of magnitude faster, has improved accuracy, includes a graphical user interface, and can produce volumetric density maps for improved pocket analysis. To demonstrate the utility of the algorithm, we use it to analyze the binding pocket of RNA editing ligase 1 from the unicellular parasite Trypanosoma brucei, the etiological agent of African sleeping sickness. The POVME analysis characterizes the full dynamics of a potentially druggable transient binding pocket and so may guide future antitrypanosomal drug-discovery efforts. We are hopeful that this new version will be a useful tool for the computational- and medicinal-chemist community.
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