Caver web: identification of tunnels and channels in proteins
and analysis of ligand transport

a 2019

Caver web: identification of tunnels and channels in proteins and analysis of ligand transport

ŠTOURAČ, Jan, O. VAVRA, Piia Pauliina KOKKONEN, Jiří FILIPOVIČ, Gabriela Filipa FONSECA PINTO et. al.

Basic information

Original name

Caver web: identification of tunnels and channels in proteins and analysis of ligand transport

Authors

ŠTOURAČ, Jan (203 Czech Republic, guarantor, belonging to the institution), O. VAVRA, Piia Pauliina KOKKONEN (246 Finland, belonging to the institution), Jiří FILIPOVIČ (203 Czech Republic, belonging to the institution), Gabriela Filipa FONSECA PINTO (620 Portugal), Andrea SCHENKMAYEROVÁ (703 Slovakia), Jiří DAMBORSKÝ (203 Czech Republic, belonging to the institution) and David BEDNÁŘ (203 Czech Republic, belonging to the institution)

Edition

European Biotechnology Congress, 2019

Other information

Language

English

Type of outcome

Konferenční abstrakt

Field of Study

20800 2.8 Environmental biotechnology

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.503

RIV identification code

RIV/00216224:14310/19:00113698

Organization unit

Faculty of Science

ISSN

DOI

http://dx.doi.org/10.1016/j.jbiotec.2019.05.251

UT WoS

000491118400233

Keywords in English

Caver web

Abstract

V originále

Caver Web 1.0 is a novel interactive web server suitable for comprehensive analysis of protein tunnels or channels as well as the ligands’ transport through identified access pathways. Caver Web is the first web tool allowing both these analyses within a single graphical user interface. The server is built on top of the tunnel detection tool Caver and employs newly developed CaverDock to study the ligand transport. The program is easy-to-use as the only required inputs are a protein structure for tunnel detection and optionally a list of ligands for transport analysis. The automated guidance procedures assist the users to correctly set up the calculation leading to accurate and biologically relevant results. The identified tunnels, their properties and energy profiles of passing ligands can be directly analyzed and visualized. The tool is very fast (2–20 min per job), making it suitable even for virtual screening. A simple setup and a comprehensible graphical user interface makes the tool accessible for broader scientific community. The server is freely available at https://loschmidt.chemi.muni.cz/caverweb.

Citovat

ŠTOURAČ, Jan, O. VAVRA, Piia Pauliina KOKKONEN, Jiří FILIPOVIČ, Gabriela Filipa FONSECA PINTO, Andrea SCHENKMAYEROVÁ, Jiří DAMBORSKÝ and David BEDNÁŘ. Caver web: identification of tunnels and channels in proteins and analysis of ligand transport. In European Biotechnology Congress. 2019. ISSN 0168-1656. Available from: https://dx.doi.org/10.1016/j.jbiotec.2019.05.251.

@proceedings{1647656,
   author = {Štourač, Jan and Vavra, O. and Kokkonen, Piia Pauliina and Filipovič, Jiří and Fonseca Pinto, Gabriela Filipa and Schenkmayerová, Andrea and Damborský, Jiří and Bednář, David},
   booktitle = {European Biotechnology Congress},
   doi = {http://dx.doi.org/10.1016/j.jbiotec.2019.05.251},
   keywords = {Caver web},
   language = {eng},
   title = {Caver web: identification of tunnels and channels in proteins and analysis of ligand transport},
   url = {https://doi.org/10.1016/j.jbiotec.2019.05.251},
   year = {2019}
}

TY  - CONF
ID  - 1647656
AU  - Štourač, Jan - Vavra, O. - Kokkonen, Piia Pauliina - Filipovič, Jiří - Fonseca Pinto, Gabriela Filipa - Schenkmayerová, Andrea - Damborský, Jiří - Bednář, David
PY  - 2019
TI  - Caver web: identification of tunnels and channels in proteins and analysis of ligand transport
KW  - Caver web
UR  - https://doi.org/10.1016/j.jbiotec.2019.05.251
L2  - https://doi.org/10.1016/j.jbiotec.2019.05.251
N2  - Caver Web 1.0 is a novel interactive web server suitable for comprehensive analysis of protein tunnels or channels as well as the ligands’ transport through identified access pathways. Caver Web is the first web tool allowing both these analyses within a single graphical user interface. The server is built on top of the tunnel detection tool Caver and employs newly developed CaverDock to study the ligand transport. The program is easy-to-use as the only required inputs are a protein structure for tunnel detection and optionally a list of ligands for transport analysis. The automated guidance procedures assist the users to correctly set up the calculation leading to accurate and biologically relevant results. The identified tunnels, their properties and energy profiles of passing ligands can be directly analyzed and visualized. The tool is very fast (2–20 min per job), making it suitable even for virtual screening. A simple setup and a comprehensible graphical user interface makes the tool accessible for broader scientific community. The server is freely available at https://loschmidt.chemi.muni.cz/caverweb.
ER  -

ŠTOURAČ, Jan, O. VAVRA, Piia Pauliina KOKKONEN, Jiří FILIPOVIČ, Gabriela Filipa FONSECA PINTO, Andrea SCHENKMAYEROVÁ, Jiří DAMBORSKÝ and David BEDNÁŘ. Caver web: identification of tunnels and channels in proteins and analysis of ligand transport. In \textit{European Biotechnology Congress}. 2019. ISSN~0168-1656. Available from: https://dx.doi.org/10.1016/j.jbiotec.2019.05.251.

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