a library for massive analyses of internal voids in biomolecules and ligand transport through them
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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:
- Preparatory stage including defining transformations needed for unified analyses
- Processing of input datasets of tunnel networks
- Layering tunnel clusters to get their simplified representation
- Computing distances among the layered clusters
- Clustering the layered clusters into superclusters and creating initial outputs
- Filtering superclusters and creating filtered outputs
- Processing datasets of transport events of ligands
- Layering transport events to get their simplified representation
- Assigning transport events to tunnel networks in superclusters and creating initial outputs
- 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.
TransportTools can be installed either:
- if you do not have already, get conda management system
- create new environment for transport tools: conda create --name transport_tools python=3.8
- activate the environment: conda activate transport_tools
- install TransportTools and all required dependencies: conda install transport_tools -c labbit -c conda-forge
- pip install transport_tools
Additionally, you might want to install following packages to enhance your experience using TransportTools:
- AmberTools to speed-up trajectory processing with pytraj engine; by following these instructions
- PyMCubes to enable supercluster visualization with surface: pip install --upgrade PyMCubes
- MSMS to speed-up supercluster visualization with the surface
To start using TransportTools type:
If you encounter any problems with installation, or the use of TransportTools please contact us at github.com.
Documentation can be found on github.com.
- 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
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