TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them.

Autor:	Brezovsky J; Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland.; International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland., Thirunavukarasu AS; Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland.; International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland., Surpeta B; Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland.; International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland., Sequeiros-Borja CE; Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland.; International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland., Mandal N; Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland.; International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland., Sarkar DK; Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland.; International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland., Dongmo Foumthuim CJ; Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland.; International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland., Agrawal N; Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2022 Mar 04; Vol. 38 (6), pp. 1752-1753.
DOI:	10.1093/bioinformatics/btab872
Abstrakt:	Summary: Information regarding pathways through voids in biomolecules and their roles in ligand transport is critical to our understanding of the function of many biomolecules. Recently, the advent of high-throughput molecular dynamics simulations has enabled the study of these pathways, and of rare transport events. However, the scale and intricacy of the data produced requires dedicated tools in order to conduct analyses efficiently and without excessive demand on users. To fill this gap, we developed the TransportTools, which allows the investigation of pathways and their utilization across large, simulated datasets. TransportTools also facilitates the development of custom-made analyses. Availability and Implementation: TransportTools is implemented in Python3 and distributed as pip and conda packages. The source code is available at https://github.com/labbit-eu/transport_tools. Data are available in a repository and can be accessed via a link: https://doi.org/10.5281/zenodo.5642954. Supplementary Information: Supplementary data are available at Bioinformatics online. (© The Author(s) 2021. Published by Oxford University Press.)
Databáze:	MEDLINE
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