The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
Open accessAbstract
Abstract 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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Cites
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
Scalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914
Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
Meng, X.-Y., Zhang, H.-X., Mezei, M., & Cui, M. (2011) · Current Computer Aided-Drug Design · doi:10.2174/157340911795677602 · Cited by 3,771
Bung, N., Pradhan, M., Srinivasan, H., & Bulusu, G. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003484 · Cited by 14
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Ojha, A. A., Votapka, L. W., & Amaro, R. E. (2023) · Chemical Science · doi:10.1039/d3sc04195f · Cited by 19
Self-citationLi, P., Soudackov, A. V., & Hammes-Schiffer, S. (2018) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.8b02945 · Cited by 12
Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome bd Oxidase
Seitz, C., Ahn, S.-H., Wei, H., Kyte, M., Cook, G. M., Krause, K. L., & McCammon, J. A. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c00344 · Cited by 11
Metadata
- Authors
- Durrant, J. D., Votapka, L., Sørensen, J., & Amaro, R. E.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2014-10-15
- Volume
- 10
- Issue
- 11
- Pages
- 5047-5056
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W2317863386
- Cited by
- 234
- References
- 4
- FWCI
- 16.41
- Type
- journal article
- Language
- en
- Open access
- hybrid
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