CAVER Analyst 2.0: Analysis and Visualization of Channels and
Tunnels in Protein Structures and Molecular Dynamics
Trajectories

J 2018

CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories

JURČÍK, Adam; David BEDNÁŘ; Jan BYŠKA; Sérgio Manuel MARQUES; Katarína FURMANOVÁ et. al.

Basic information

Original name

CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories

Authors

Edition

Bioinformatics, 2018, 1367-4803

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

is not subject to a state or trade secret

References:

URL

Impact factor

Impact factor: 4.531

RIV identification code

RIV/00216224:14330/18:00100952

Organization unit

Faculty of Informatics

DOI

https://doi.org/10.1093/bioinformatics/bty386

UT WoS

000448782100024

EID Scopus

2-s2.0-85054891903

Keywords in English

protein;tunnel;software;visualization

Abstract

In the original language

Motivation: Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications. Results: CAVER Analyst 2.0 is a software tool for quantitative analysis and real-time visualization of tunnels and channels in static and dynamic structures. This version provides the users with many new functions, including advanced techniques for intuitive visual inspection of the spatiotemporal behavior of tunnels and channels. Novel integrated algorithms allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations. Availability and implementation: CAVER Analyst 2.0 is a multi-platform standalone Java-based application. Binaries and documentation are freely available at www.caver.cz.

Links

GA16-06096S, research and development project

Name: Objasnění významu dynamických tunelů pro enzymatickou katalýzu: simulace a fluorescenční experimenty

Investor: Czech Science Foundation

GA17-07690S, research and development project

Name: Metody identifikace a vizualizace tunelů pro flexibilní ligandy v dynamických proteinech (Acronym: FLigComp)

Investor: Czech Science Foundation

LM2015047, research and development project

Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

Investor: Ministry of Education, Youth and Sports of the CR

LO1214, research and development project

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX)

Investor: Ministry of Education, Youth and Sports of the CR

Cite

JURČÍK, Adam; David BEDNÁŘ; Jan BYŠKA; Sérgio Manuel MARQUES; Katarína FURMANOVÁ; Lukáš DANIEL; Piia Pauliina KOKKONEN; Jan BREZOVSKÝ; Ondřej STRNAD; Jan ŠTOURAČ; Antonín PAVELKA; Martin MANAK; Jiří DAMBORSKÝ and Barbora KOZLÍKOVÁ. CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Bioinformatics. 2018, vol. 34, No 20, p. 3586-3588. ISSN 1367-4803. Available from: https://doi.org/10.1093/bioinformatics/bty386.

@article{1418320,
   author = {Jurčík, Adam and Bednář, David and Byška, Jan and Marques, Sérgio Manuel and Furmanová, Katarína and Daniel, Lukáš and Kokkonen, Piia Pauliina and Brezovský, Jan and Strnad, Ondřej and Štourač, Jan and Pavelka, Antonín and Manak, Martin and Damborský, Jiří and Kozlíková, Barbora},
   article_number = {20},
   doi = {https://doi.org/10.1093/bioinformatics/bty386},
   keywords = {protein;tunnel;software;visualization},
   language = {eng},
   issn = {1367-4803},
   journal = {Bioinformatics},
   title = {CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories},
   url = {http://dx.doi.org/10.1093/bioinformatics/bty386},
   volume = {34},
   year = {2018}
}

TY  - JOUR
ID  - 1418320
AU  - Jurčík, Adam - Bednář, David - Byška, Jan - Marques, Sérgio Manuel - Furmanová, Katarína - Daniel, Lukáš - Kokkonen, Piia Pauliina - Brezovský, Jan - Strnad, Ondřej - Štourač, Jan - Pavelka, Antonín - Manak, Martin - Damborský, Jiří - Kozlíková, Barbora
PY  - 2018
TI  - CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories
JF  - Bioinformatics
VL  - 34
IS  - 20
SP  - 3586-3588
EP  - 3586-3588
SN  - 13674803
KW  - protein;tunnel;software;visualization
UR  - http://dx.doi.org/10.1093/bioinformatics/bty386
N2  - Motivation: Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications. Results: CAVER Analyst 2.0 is a software tool for quantitative analysis and real-time visualization of tunnels and channels in static and dynamic structures. This version provides the users with many new functions, including advanced techniques for intuitive visual inspection of the spatiotemporal behavior of tunnels and channels. Novel integrated algorithms allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations. Availability and implementation: CAVER Analyst 2.0 is a multi-platform standalone Java-based application. Binaries and documentation are freely available at www.caver.cz.
ER  -

JURČÍK, Adam; David BEDNÁŘ; Jan BYŠKA; Sérgio Manuel MARQUES; Katarína FURMANOVÁ; Lukáš DANIEL; Piia Pauliina KOKKONEN; Jan BREZOVSKÝ; Ondřej STRNAD; Jan ŠTOURAČ; Antonín PAVELKA; Martin MANAK; Jiří DAMBORSKÝ and Barbora KOZLÍKOVÁ. CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. \textit{Bioinformatics}. 2018, vol.~34, No~20, p.~3586-3588. ISSN~1367-4803. Available from: https://doi.org/10.1093/bioinformatics/bty386.

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