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.

Základní údaje

Originální název

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

Název česky

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

Autoři

PETŘEK, Martin (203 Česká republika), Michal OTYEPKA (203 Česká republika), Pavel BANÁŠ (203 Česká republika), Jaroslav KOČA (203 Česká republika) a Jiří DAMBORSKÝ (203 Česká republika, garant)

Vydání

BMC BIOINFORMATICS, 2006, 1471-2105

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10404 Polymer science

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.617

Kód RIV

RIV/00216224:14310/06:00017454

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000239737800001

Klíčová slova anglicky

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

Štítky

CAVER program, clefts, pockets and cavities, PROTEIN

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 22. 3. 2010 09:10, prof. Mgr. Jiří Damborský, Dr.

Anotace

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.

Česky

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

Návaznosti

MSM0021622413, záměr

Název: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Proteiny v metabolismu a při interakci organismů s prostředím

Citovat

PETŘEK, Martin, Michal OTYEPKA, Pavel BANÁŠ, Jaroslav KOČA a Jiří DAMBORSKÝ. CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities. BMC BIOINFORMATICS. 2006, roč. 7, č. 7, s. 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 a Jiří DAMBORSKÝ. CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities. \textit{BMC BIOINFORMATICS}. 2006, roč.~7, č.~7, s.~316-324. ISSN~1471-2105.

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