Simulation of Ligand Transport in Receptors Using CaverDock

C 2021

Simulation of Ligand Transport in Receptors Using CaverDock

HOZZOVÁ, Jana, Ondřej VÁVRA, David BEDNÁŘ and Jiří FILIPOVIČ

Basic information

Original name

Simulation of Ligand Transport in Receptors Using CaverDock

Authors

HOZZOVÁ, Jana (703 Slovakia, belonging to the institution), Ondřej VÁVRA (203 Czech Republic, belonging to the institution), David BEDNÁŘ (203 Czech Republic, belonging to the institution) and Jiří FILIPOVIČ (203 Czech Republic, guarantor, belonging to the institution)

Edition

New York, Protein-Ligand Interactions and Drug Design, p. 105-124, 20 pp. Methods in Molecular Biology, vol 2266, 2021

Publisher

Humana, New York, NY

Other information

Language

English

Type of outcome

Kapitola resp. kapitoly v odborné knize

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

References:

URL

RIV identification code

RIV/00216224:14610/21:00118914

Organization unit

Institute of Computer Science

ISBN

978-1-0716-1208-8

DOI

http://dx.doi.org/10.1007/978-1-0716-1209-5_6

UT WoS

000683472300007

Keywords in English

Tunnel analysis; Ligand transport; Molecular docking; Drug design; Enzyme engineering; Ligand screening

Abstract

V originále

Interactions between enzymes and small molecules lie in the center of many fundamental biochemical processes. Their analysis using molecular dynamics simulations have high computational demands, geometric approaches fail to consider chemical forces, and molecular docking offers only static information. Recently, we proposed to combine molecular docking and geometric approaches in an application called CaverDock. CaverDock is discretizing enzyme tunnel into discs, iteratively docking with restraints into one disc after another and searching for a trajectory of the ligand passing through the tunnel. Here, we focus on the practical side of its usage describing the whole method: from getting the application, and processing the data through a workflow, to interpreting the results. Moreover, we shared the best practices, recommended how to solve the most common issues, and demonstrated its application on three use cases.

Links

GJ20-15915Y, research and development project

Name: Studium molekulováho rozpoznávání a vývoj nových softwarových nástrojů pro identifikaci a design přístupových cest v proteinech

Investor: Czech Science Foundation

LM2015085, research and development project

Name: CERIT Scientific Cloud (Acronym: CERIT-SC)

Investor: Ministry of Education, Youth and Sports of the CR, CERIT Scientific Cloud

90042, large research infrastructures

Name: CESNET II

Citovat

HOZZOVÁ, Jana, Ondřej VÁVRA, David BEDNÁŘ and Jiří FILIPOVIČ. Simulation of Ligand Transport in Receptors Using CaverDock. In Flavio Ballante. Protein-Ligand Interactions and Drug Design. New York: Humana, New York, NY, 2021, p. 105-124. Methods in Molecular Biology, vol 2266. ISBN 978-1-0716-1208-8. Available from: https://dx.doi.org/10.1007/978-1-0716-1209-5_6.

@inbook{1757928,
   author = {Hozzová, Jana and Vávra, Ondřej and Bednář, David and Filipovič, Jiří},
   address = {New York},
   booktitle = {Protein-Ligand Interactions and Drug Design},
   doi = {http://dx.doi.org/10.1007/978-1-0716-1209-5_6},
   editor = {Flavio Ballante},
   keywords = {Tunnel analysis; Ligand transport; Molecular docking; Drug design; Enzyme engineering; Ligand screening},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {New York},
   isbn = {978-1-0716-1208-8},
   pages = {105-124},
   publisher = {Humana, New York, NY},
   title = {Simulation of Ligand Transport in Receptors Using CaverDock},
   url = {https://doi.org/10.1007/978-1-0716-1209-5_6},
   year = {2021}
}

TY  - CHAP
ID  - 1757928
AU  - Hozzová, Jana - Vávra, Ondřej - Bednář, David - Filipovič, Jiří
PY  - 2021
TI  - Simulation of Ligand Transport in Receptors Using CaverDock
VL  - Methods in Molecular Biology, vol 2266
PB  - Humana, New York, NY
CY  - New York
SN  - 9781071612088
KW  - Tunnel analysis
KW  - Ligand transport
KW  - Molecular docking
KW  - Drug design
KW  - Enzyme engineering
KW  - Ligand screening
UR  - https://doi.org/10.1007/978-1-0716-1209-5_6
N2  - Interactions between enzymes and small molecules lie in the center of many fundamental biochemical processes. Their analysis using molecular dynamics simulations have high computational demands, geometric approaches fail to consider chemical forces, and molecular docking offers only static information. Recently, we proposed to combine molecular docking and geometric approaches in an application called CaverDock. CaverDock is discretizing enzyme tunnel into discs, iteratively docking with restraints into one disc after another and searching for a trajectory of the ligand passing through the tunnel. Here, we focus on the practical side of its usage describing the whole method: from getting the application, and processing the data through a workflow, to interpreting the results. Moreover, we shared the best practices, recommended how to solve the most common issues, and demonstrated its application on three use cases.
ER  -

HOZZOVÁ, Jana, Ondřej VÁVRA, David BEDNÁŘ and Jiří FILIPOVIČ. Simulation of Ligand Transport in Receptors Using CaverDock. In Flavio Ballante. \textit{Protein-Ligand Interactions and Drug Design}. New York: Humana, New York, NY, 2021, p.~105-124. Methods in Molecular Biology, vol 2266. ISBN~978-1-0716-1208-8. Available from: https://dx.doi.org/10.1007/978-1-0716-1209-5\_{}6.

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