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MOLE 2.0: advanced approach for analysis of biomacromolecular channels

BACKGROUND: Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. RESULTS: We present an advanced software tool entitled MOLE 2.0, which has been designed to analyze mo...

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Autores principales: Sehnal, David, Svobodová Vařeková, Radka, Berka, Karel, Pravda, Lukáš, Navrátilová, Veronika, Banáš, Pavel, Ionescu, Crina-Maria, Otyepka, Michal, Koča, Jaroslav
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765717/
https://www.ncbi.nlm.nih.gov/pubmed/23953065
http://dx.doi.org/10.1186/1758-2946-5-39
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author Sehnal, David
Svobodová Vařeková, Radka
Berka, Karel
Pravda, Lukáš
Navrátilová, Veronika
Banáš, Pavel
Ionescu, Crina-Maria
Otyepka, Michal
Koča, Jaroslav
author_facet Sehnal, David
Svobodová Vařeková, Radka
Berka, Karel
Pravda, Lukáš
Navrátilová, Veronika
Banáš, Pavel
Ionescu, Crina-Maria
Otyepka, Michal
Koča, Jaroslav
author_sort Sehnal, David
collection PubMed
description BACKGROUND: Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. RESULTS: We present an advanced software tool entitled MOLE 2.0, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.0 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability. We also assessed the variability in physicochemical properties of eighty X-ray structures of two members of the cytochrome P450 superfamily. CONCLUSION: Estimated physicochemical properties of the identified channels in the selected biomacromolecules corresponded well with the known functions of the respective channels. Thus, the predicted physicochemical properties may provide useful information about the potential functions of identified channels. The MOLE 2.0 software is available at http://mole.chemi.muni.cz.
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spelling pubmed-37657172013-09-11 MOLE 2.0: advanced approach for analysis of biomacromolecular channels Sehnal, David Svobodová Vařeková, Radka Berka, Karel Pravda, Lukáš Navrátilová, Veronika Banáš, Pavel Ionescu, Crina-Maria Otyepka, Michal Koča, Jaroslav J Cheminform Software BACKGROUND: Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. RESULTS: We present an advanced software tool entitled MOLE 2.0, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.0 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability. We also assessed the variability in physicochemical properties of eighty X-ray structures of two members of the cytochrome P450 superfamily. CONCLUSION: Estimated physicochemical properties of the identified channels in the selected biomacromolecules corresponded well with the known functions of the respective channels. Thus, the predicted physicochemical properties may provide useful information about the potential functions of identified channels. The MOLE 2.0 software is available at http://mole.chemi.muni.cz. BioMed Central 2013-08-16 /pmc/articles/PMC3765717/ /pubmed/23953065 http://dx.doi.org/10.1186/1758-2946-5-39 Text en Copyright © 2013 Sehnal et al.; licensee Chemistry Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Sehnal, David
Svobodová Vařeková, Radka
Berka, Karel
Pravda, Lukáš
Navrátilová, Veronika
Banáš, Pavel
Ionescu, Crina-Maria
Otyepka, Michal
Koča, Jaroslav
MOLE 2.0: advanced approach for analysis of biomacromolecular channels
title MOLE 2.0: advanced approach for analysis of biomacromolecular channels
title_full MOLE 2.0: advanced approach for analysis of biomacromolecular channels
title_fullStr MOLE 2.0: advanced approach for analysis of biomacromolecular channels
title_full_unstemmed MOLE 2.0: advanced approach for analysis of biomacromolecular channels
title_short MOLE 2.0: advanced approach for analysis of biomacromolecular channels
title_sort mole 2.0: advanced approach for analysis of biomacromolecular channels
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765717/
https://www.ncbi.nlm.nih.gov/pubmed/23953065
http://dx.doi.org/10.1186/1758-2946-5-39
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