CAVER: A New Tool to Explore Routes from Protein Clefts,
Pockets and Cavities

J 2006

CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities

PETŘEK, Martin, Michal OTYEPKA, Pavel BANÁŠ, Jaroslav KOČA, Jiří DAMBORSKÝ et. al.

Basic information

Original name

CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities

Name in Czech

CAVER" nový nástroj pro průzkum cest z proteinových kapes a dutin.

Authors

PETŘEK, Martin (203 Czech Republic), Michal OTYEPKA (203 Czech Republic), Pavel BANÁŠ (203 Czech Republic), Jaroslav KOČA (203 Czech Republic) and Jiří DAMBORSKÝ (203 Czech Republic, guarantor)

Edition

BMC BIOINFORMATICS, 2006, 1471-2105

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10404 Polymer science

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.617

RIV identification code

RIV/00216224:14310/06:00017454

Organization unit

Faculty of Science

UT WoS

000239737800001

Keywords in English

protein; clefts; pockets and cavities; CAVER program; crystallographic analysis and NMR experiments

Abstract

ORIG CZ

V originále

BACKGROUND. The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent. RESULTS. The algorithm to perform a skeleton search was based on a reciprocal distance function grid that was developed and implemented for the CAVER program. The program identifies and visualizes routes from the interior of the protein to the bulk solvent. CAVER was primarily developed for proteins, but the algorithm is sufficiently robust to allow the analysis of any molecular system, including nucleic acids or inorganic material. Calculations can be performed using discrete structures from crystallographic analysis and NMR experiments as well as with trajectories from molecular dynamics simulations. The fully functional program is available as a stand-alone version and as plug-in for the molecular modeling program PyMol. Additionally, selected functions are accessible in an online version. CONCLUSIONS. The algorithm developed automatically finds the path from a starting point located within the interior of a protein. The algorithm is sufficiently rapid and robust to enable routine analysis of molecular dynamics trajectories containing thousands of snapshots. The algorithm is based on reciprocal metrics and provides an easy method to find a centerline, i.e. the spine, of complicated objects such as a protein tunnel. It can also be applied to many other molecules.

In Czech

Hlavním cílem této studie bylo vyvinout algoritmus pro rychlou, precizní a automatickou identifikaci cest, vedoucích z proteinových zakoutí, dutin a kapes.

Links

MSM0021622413, plan (intention)

Name: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment

Citovat

PETŘEK, Martin, Michal OTYEPKA, Pavel BANÁŠ, Jaroslav KOČA and Jiří DAMBORSKÝ. CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities. BMC BIOINFORMATICS. 2006, vol. 7, No 7, p. 316-324. ISSN 1471-2105.

@article{700051,
   author = {Petřek, Martin and Otyepka, Michal and Banáš, Pavel and Koča, Jaroslav and Damborský, Jiří},
   article_number = {7},
   keywords = {protein; clefts; pockets and cavities; CAVER program; crystallographic analysis and NMR experiments},
   language = {eng},
   issn = {1471-2105},
   journal = {BMC BIOINFORMATICS},
   title = {CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities},
   url = {http://loschmidt.chemi.muni.cz/peg/abstracts/bmcbioinf06.html},
   volume = {7},
   year = {2006}
}

TY  - JOUR
ID  - 700051
AU  - Petřek, Martin - Otyepka, Michal - Banáš, Pavel - Koča, Jaroslav - Damborský, Jiří
PY  - 2006
TI  - CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities
JF  - BMC BIOINFORMATICS
VL  - 7
IS  - 7
SP  - 316
EP  - 316
SN  - 14712105
KW  - protein
KW  - clefts
KW  - pockets and cavities
KW  - CAVER program
KW  - crystallographic analysis and NMR experiments
UR  - http://loschmidt.chemi.muni.cz/peg/abstracts/bmcbioinf06.html
N2  - BACKGROUND. The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent. RESULTS. The algorithm to perform a skeleton search was based on a reciprocal distance function grid that was developed and implemented for the CAVER program. The program identifies and visualizes routes from the interior of the protein to the bulk solvent. CAVER was primarily developed for proteins, but the algorithm is sufficiently robust to allow the analysis of any molecular system, including nucleic acids or inorganic material. Calculations can be performed using discrete structures from crystallographic analysis and NMR experiments as well as with trajectories from molecular dynamics simulations. The fully functional program is available as a stand-alone version and as plug-in for the molecular modeling program PyMol. Additionally, selected functions are accessible in an online version. CONCLUSIONS. The algorithm developed automatically finds the path from a starting point located within the interior of a protein. The algorithm is sufficiently rapid and robust to enable routine analysis of molecular dynamics trajectories containing thousands of snapshots. The algorithm is based on reciprocal metrics and provides an easy method to find a centerline, i.e. the spine, of complicated objects such as a protein tunnel. It can also be applied to many other molecules.
ER  -

PETŘEK, Martin, Michal OTYEPKA, Pavel BANÁŠ, Jaroslav KOČA and Jiří DAMBORSKÝ. CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities. \textit{BMC BIOINFORMATICS}. 2006, vol.~7, No~7, p.~316-324. ISSN~1471-2105.

Detailed Information on Publication Record