Dataset Information

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

ABSTRACT:

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.

SUBMITTER: Brezovsky J

PROVIDER: S-EPMC8896600 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Brezovsky Jan J Thirunavukarasu Aravind Selvaram AS Surpeta Bartlomiej B Sequeiros-Borja Carlos Eduardo CE Mandal Nishita N Sarkar Dheeraj Kumar DK Dongmo Foumthuim Cedrix J CJ Agrawal Nikhil N

Bioinformatics (Oxford, England) 20220301 6

<h4>Summary</h4>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 ga ...[more]

PMID: 34971366

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Dataset Information

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

Summary

Availability and implementation

Supplementary information

Publications

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

Similar Datasets

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