Voronoi-Based Detection of Pockets in Proteins Defined by Large and Small Probes

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F49777513%3A23520%2F19%3A43955182" target="_blank" >RIV/49777513:23520/19:43955182 - isvavai.cz</a>

Result on the web

<a href="https://doi.org/10.1002/jcc.25828" target="_blank" >https://doi.org/10.1002/jcc.25828</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/jcc.25828" target="_blank" >10.1002/jcc.25828</a>

Result language

angličtina

Original language name

Voronoi-Based Detection of Pockets in Proteins Defined by Large and Small Probes

Original language description

The function of enzymatic proteins is given by their ability to bind specific small molecules into their active sites. These sites can often be found in pockets on a hypothetical boundary between the protein and its environment. Detection, analysis, and visualization of pockets find its use in protein engineering and drug discovery. Many definitions of pockets and algorithms for their computation have been proposed. Kawabata and Go defined them as the regions of empty space into which a small spherical probe can enter but a large probe cannot and developed programs that can compute their approximate shape. In this article, this definition was slightly modified in order to capture the existence of large internal holes, and a Voronoi‐based method for the computation of the exact shape of these modified regions is introduced. The method first puts a finite number of large probes on the protein exterior surface and then, considering both large probes and atomic balls as obstacles for the small probe, the method computes the exact shape of the regions for the small probe. This is all achieved with Voronoi diagrams, which help with the safe navigation of spherical probes among spherical obstacles. Detected regions are internally represented as graphs of vertices and edges describing possible movements of the center of the small probe on Voronoi edges. The surface bounding each region is obtained from this representation and used for visualization, volume estimation, and comparison with other approaches.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2019

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Computational Chemistry

ISSN

0192-8651

e-ISSN

—

Volume of the periodical

40

Issue of the periodical within the volume

19

Country of publishing house

US - UNITED STATES

Number of pages

14

Pages from-to

1758-1771

UT code for WoS article

000470013600003

EID of the result in the Scopus database

2-s2.0-85063670773