MOLE 2.0: advanced approach for analysis of biomacromolecular channels
By David Sehnal, Radka Svobodová Vareková, Karel Berka, Lukás Pravda, Veronika Navrátilová, Pavel Banás, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koca. Journal of Cheminformatics, 2013
316 citations recorded by the source corpus.
BackgroundChannels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity.ResultsWe 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.ConclusionEstimated 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.
Subfields: Computational Theory and Mathematics, Pharmacology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/373ba7009a1f95711b63b9b1c3970a35ee70de96
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In Computational Theory and Mathematics
In Pharmacology
In Spectroscopy
Citations in the corpus
- MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update) (2018, methodology): “Each profile can be colored according to the physicochemical properties (16,18) of the lining amino acids.”
- PDBsum: Structural summaries of PDB entries (2017, methodology): “Other analyses performed by PDBsum, but not shown in Figures 1–3, include calculation of protein pores and tunnels by the Mole 2.0 program, 38 and validation of any bound ligands by MotiveValidator.”