MOLEonline 2.0: Interactive Web-based Analysis of
Biomacromolecular Channels

J 2012

MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels

BERKA, Karel, Ondřej HANÁK, David SEHNAL, Pavel BANÁŠ, Veronika NAVRÁTILOVÁ et. al.

Basic information

Original name

MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels

Authors

BERKA, Karel (203 Czech Republic, guarantor), Ondřej HANÁK (203 Czech Republic), David SEHNAL (203 Czech Republic, belonging to the institution), Pavel BANÁŠ (203 Czech Republic), Veronika NAVRÁTILOVÁ (203 Czech Republic), Deepti JAISWAL (356 India, belonging to the institution), Crina-Maria IONESCU (642 Romania, belonging to the institution), Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, belonging to the institution), Jaroslav KOČA (203 Czech Republic, belonging to the institution) and Michal OTYEPKA (203 Czech Republic)

Edition

Nucleic Acids Research, Oxford, UK, Oxford Press, 2012, 0305-1048

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 8.278

RIV identification code

RIV/00216224:14740/12:00057571

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/nar/gks363

UT WoS

000306670900036

Keywords in English

CYTOCHROMES P450; PROTEIN STRUCTURES; NUCLEIC-ACIDS; SUBSTRATE PREFERENCES; POTASSIUM CHANNEL; PHOTOSYSTEM-II; ACTIVE-SITES; IDENTIFICATION; TUNNELS; MACROMOLECULES

Abstract

V originále

Biomolecular channels play important roles in many biological systems, e.g. enzymes, ribosomes and ion channels. This article introduces a web-based interactive MOLEonline 2.0 application for the analysis of access/egress paths to interior molecular voids. MOLEonline 2.0 enables platform-independent, easy-to-use and interactive analyses of (bio)macromolecular channels, tunnels and pores. Results are presented in a clear manner, making their interpretation easy. For each channel, MOLEonline displays a 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties. The users can tune advanced parameters when performing a channel search to direct the search according to their needs. The MOLEonline 2.0 application is freely available via the Internet at http://ncbr.muni.cz/mole or http://mole.upol.cz.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

GD301/09/H004, research and development project

Name: Molekulární a strukturní biologie vybraných cytostatik. Od mechanistických studií k chemoterapii rakoviny

Investor: Czech Science Foundation

ME08008, research and development project

Name: Návrh antibakteriálních a antivirových léků na bázi cukrů a glykomimetik

Investor: Ministry of Education, Youth and Sports of the CR, Design of Carbohydrates and Glycomimetics as Antibacterial and Antiviral Drugs, Research and Development Programme KONTAKT (ME)

MUNI/A/0914/2009, interní kód MU

Name: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace (Acronym: SV-FI MAV)

Investor: Masaryk University, Category A

286154, interní kód MU

Name: SYLICA - Synergies of Life and Material Sciences to Create a New Future (Acronym: SYLICA)

Investor: European Union, Capacities

Citovat

BERKA, Karel, Ondřej HANÁK, David SEHNAL, Pavel BANÁŠ, Veronika NAVRÁTILOVÁ, Deepti JAISWAL, Crina-Maria IONESCU, Radka SVOBODOVÁ VAŘEKOVÁ, Jaroslav KOČA and Michal OTYEPKA. MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels. Nucleic Acids Research. Oxford, UK: Oxford Press, 2012, vol. 40, W1, p. "W222"–"W227", 6 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gks363.

@article{991130,
   author = {Berka, Karel and Hanák, Ondřej and Sehnal, David and Banáš, Pavel and Navrátilová, Veronika and Jaiswal, Deepti and Ionescu, CrinaandMaria and Svobodová Vařeková, Radka and Koča, Jaroslav and Otyepka, Michal},
   article_location = {Oxford, UK},
   article_number = {W1},
   doi = {http://dx.doi.org/10.1093/nar/gks363},
   keywords = {CYTOCHROMES P450; PROTEIN STRUCTURES; NUCLEIC-ACIDS; SUBSTRATE PREFERENCES; POTASSIUM CHANNEL; PHOTOSYSTEM-II; ACTIVE-SITES; IDENTIFICATION; TUNNELS; MACROMOLECULES},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels},
   url = {http://nar.oxfordjournals.org/content/40/W1/W222.full},
   volume = {40},
   year = {2012}
}

TY  - JOUR
ID  - 991130
AU  - Berka, Karel - Hanák, Ondřej - Sehnal, David - Banáš, Pavel - Navrátilová, Veronika - Jaiswal, Deepti - Ionescu, Crina-Maria - Svobodová Vařeková, Radka - Koča, Jaroslav - Otyepka, Michal
PY  - 2012
TI  - MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels
JF  - Nucleic Acids Research
VL  - 40
IS  - W1
SP  - "W222"–"W227"
EP  - "W222"–"W227"
PB  - Oxford Press
SN  - 03051048
KW  - CYTOCHROMES P450
KW  - PROTEIN STRUCTURES
KW  - NUCLEIC-ACIDS
KW  - SUBSTRATE PREFERENCES
KW  - POTASSIUM CHANNEL
KW  - PHOTOSYSTEM-II
KW  - ACTIVE-SITES
KW  - IDENTIFICATION
KW  - TUNNELS
KW  - MACROMOLECULES
UR  - http://nar.oxfordjournals.org/content/40/W1/W222.full
L2  - http://nar.oxfordjournals.org/content/40/W1/W222.full
N2  - Biomolecular channels play important roles in many biological systems, e.g. enzymes, ribosomes and ion channels. This article introduces a web-based interactive MOLEonline 2.0 application for the analysis of access/egress paths to interior molecular voids. MOLEonline 2.0 enables platform-independent, easy-to-use and interactive analyses of (bio)macromolecular channels, tunnels and pores. Results are presented in a clear manner, making their interpretation easy. For each channel, MOLEonline displays a 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties. The users can tune advanced parameters when performing a channel search to direct the search according to their needs. The MOLEonline 2.0 application is freely available via the Internet at http://ncbr.muni.cz/mole or http://mole.upol.cz.
ER  -

BERKA, Karel, Ondřej HANÁK, David SEHNAL, Pavel BANÁŠ, Veronika NAVRÁTILOVÁ, Deepti JAISWAL, Crina-Maria IONESCU, Radka SVOBODOVÁ VAŘEKOVÁ, Jaroslav KOČA and Michal OTYEPKA. MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels. \textit{Nucleic Acids Research}. Oxford, UK: Oxford Press, 2012, vol.~40, W1, p.~''W222''–''W227'', 6 pp. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gks363.

Detailed Information on Publication Record