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POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics

[Image: see text] 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 chara...

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Autores principales: Durrant, Jacob D., Votapka, Lane, Sørensen, Jesper, Amaro, Rommie E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2014
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230373/
https://www.ncbi.nlm.nih.gov/pubmed/25400521
http://dx.doi.org/10.1021/ct500381c
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author Durrant, Jacob D.
Votapka, Lane
Sørensen, Jesper
Amaro, Rommie E.
author_facet Durrant, Jacob D.
Votapka, Lane
Sørensen, Jesper
Amaro, Rommie E.
author_sort Durrant, Jacob D.
collection PubMed
description [Image: see text] 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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spelling pubmed-42303732015-09-29 POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics Durrant, Jacob D. Votapka, Lane Sørensen, Jesper Amaro, Rommie E. J Chem Theory Comput [Image: see text] 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. American Chemical Society 2014-09-29 2014-11-11 /pmc/articles/PMC4230373/ /pubmed/25400521 http://dx.doi.org/10.1021/ct500381c Text en Copyright © 2014 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes.
spellingShingle Durrant, Jacob D.
Votapka, Lane
Sørensen, Jesper
Amaro, Rommie E.
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
title POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
title_full POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
title_fullStr POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
title_full_unstemmed POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
title_short POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
title_sort povme 2.0: an enhanced tool for determining pocket shape and volume characteristics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230373/
https://www.ncbi.nlm.nih.gov/pubmed/25400521
http://dx.doi.org/10.1021/ct500381c
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