transport-tools 0.9.5

a library for massive analyses of internal voids in biomolecules and ligand transport through them

TransportTools

TransportTools library builds on and extends results of CAVER and AQUA-DUCT analyses to provide comprehensive insights into molecular details of transport processes related to biomolecules.

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Overview

Using the TransportTools engine, end-users can get access to

• efficient analyses of molecular tunnels in extensive MD simulations, including those originating from massively parallel calculations or very long simulations,
• information on molecular voids in the biomolecules with their actual utilization by small molecules,
• rigorous comparison of transport processes in different simulation sets, e.g., contrasting transport in the original system and system perturbed by mutations, different solvents, presence of ligands, etc.

From a programmatic point of view, the library will also help to

• simplify custom-made analyses of transport processes, application of various filters on explored molecular voids,
• facilitate further development of tools focusing on the study of transport processes by providing a rich environment and interface to the popular packages in the field.

Currently, TransportTools engine can perform its action in 10 consecutive stages:

1. Preparatory stage including defining transformations needed for unified analyses
2. Processing of input datasets of tunnel networks
3. Layering tunnel clusters to get their simplified representation
4. Computing distances among the layered clusters
5. Clustering the layered clusters into superclusters and creating initial outputs
6. Filtering superclusters and creating filtered outputs
7. Processing datasets of transport events of ligands
8. Layering transport events to get their simplified representation
9. Assigning transport events to tunnel networks in superclusters and creating initial outputs
10. Filtering supercluster with events and creating filtered outputs with events

Note that stages 7-10 depend on the availability of data on transport events from AQUA-DUCT and hence are optional.

Availability

TransportTools is licensed under: GNU GPL v3 license, and the source code is available at github.com.

Installation

TransportTools can be installed either:

via CONDA:

1. if you do not have already, get conda management system
2. create new environment for transport tools: conda create --name transport_tools python=3.8
3. activate the environment: conda activate transport_tools
4. install TransportTools and all required dependencies: conda install transport_tools -c labbit -c conda-forge

or PyPi:

1. pip install transport_tools

Additionally, you might want to install following packages to enhance your experience using TransportTools:

1. AmberTools to speed-up trajectory processing with pytraj engine; by following these instructions
2. PyMCubes to enable supercluster visualization with surface: pip install --upgrade PyMCubes
3. MSMS to speed-up supercluster visualization with the surface

To start using TransportTools type:

tt_engine.py --help

Troubleshooting

If you encounter any problems with installation, or the use of TransportTools please contact us at github.com.

Documentation

Documentation can be found on github.com.

References

• Brezovsky et al, 2022: TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them. Bioinformatics 38: 1752-1753
• Sequeiros-Borja et al, 2023: Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations, MethodsX 10C: 101968

Funding

The initial development of this library was funded by the National Science Centre, Poland - grant no. 2017/25/B/NZ1/01307 and 2017/26/E/NZ1/00548.