CHOVANCOVÁ, Eva, Antonín PAVELKA, Petr BENEŠ, Ondřej STRNAD, Jan BREZOVSKÝ, Barbora KOZLÍKOVÁ, Artur Wiktor GORA, Vilém ŠUSTR, Martin KLVAŇA, Petr MEDEK, Lada BIEDERMANNOVÁ, Jiří SOCHOR and Jiří DAMBORSKÝ. CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures. PLoS Computational Biology, 2012, vol. 8, No 10, p. "nestránkováno". ISSN 1553-7358. doi:10.1371/journal.pcbi.1002708.
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Basic information
Original name CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
Name in Czech CAVER 3.0: nástroj pro analýzu transportních cest v dynamických proteinových strukturách
Authors CHOVANCOVÁ, Eva (203 Czech Republic, belonging to the institution), Antonín PAVELKA (203 Czech Republic, belonging to the institution), Petr BENEŠ (203 Czech Republic, belonging to the institution), Ondřej STRNAD (203 Czech Republic, belonging to the institution), Jan BREZOVSKÝ (203 Czech Republic, belonging to the institution), Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution), Artur Wiktor GORA (616 Poland, belonging to the institution), Vilém ŠUSTR (203 Czech Republic, belonging to the institution), Martin KLVAŇA (203 Czech Republic, belonging to the institution), Petr MEDEK (203 Czech Republic, belonging to the institution), Lada BIEDERMANNOVÁ (203 Czech Republic, belonging to the institution), Jiří SOCHOR (203 Czech Republic, belonging to the institution) and Jiří DAMBORSKÝ (203 Czech Republic, guarantor, belonging to the institution).
Edition PLoS Computational Biology, 2012, 1553-7358.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10600 1.6 Biological sciences
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 4.867
RIV identification code RIV/00216224:14310/12:00057117
Organization unit Faculty of Science
Doi http://dx.doi.org/10.1371/journal.pcbi.1002708
UT WoS 000310568800009
Keywords in English software tool; tunnel; channel; structural analysis; protein design; drug design; CAVER; dynamics
Tags AKR, best, rivok
Tags International impact, Reviewed
Changed by Changed by: Ing. Andrea Mikešková, učo 137293. Changed: 12/4/2013 13:20.
Abstract
Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz.
Links
ED0001/01/01, research and development projectName: CETOCOEN
GAP202/10/1435, research and development projectName: Analýza a vizualizace proteinových struktur
Investor: Czech Science Foundation, Standard Projects
GAP503/12/0572, research and development projectName: Konstrukce syntetické metabolické dráhy pro degradaci důležitého environmentálního polutantu proteinovým a metabolickým inženýrstvím
Investor: Czech Science Foundation, Standard Projects
IAA401630901, research and development projectName: Evoluce substrátové specifity u enzymů aktivních s xenobiotickými látkami
Investor: Academy of Sciences of the Czech Republic, Grants of distinctly investigative character focused on the sphere of research pursued at present particularly in the ASCR
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journal.pcbi.1002708.pdf Licence Creative Commons  File version Kozlíková, B. 23/10/2012

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Right to administer:
  • a concrete person RNDr. Lada Biedermannová, Ph.D., učo 110600
  • a concrete person Artur Wiktor Góra, PhD., učo 114009
  • a concrete person Ing. Andrea Mikešková, učo 137293
  • a concrete person RNDr. Ondřej Strnad, Ph.D., učo 139568
  • a concrete person Mgr. Vilém Šustr, učo 140485
  • a concrete person prof. Mgr. Jiří Damborský, Dr., učo 1441
  • a concrete person prof. Ing. Jiří Sochor, CSc., učo 2446
  • a concrete person Mgr. Petr Medek, učo 39593
  • a concrete person Mgr. Martin Klvaňa, Ph.D., učo 39995
  • a concrete person Mgr. Eva Šebestová, Ph.D., učo 40707
  • a concrete person doc. RNDr. Barbora Kozlíková, Ph.D., učo 60850
  • a concrete person RNDr. Petr Beneš, Ph.D., učo 60865
  • a concrete person Mgr. Jan Brezovský, Ph.D., učo 64097
  • a concrete person RNDr. Antonín Pavelka, Ph.D., učo 99207
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