Package: transport-tools
TransportToolsTransportToolslibrary builds on and extends results ofCAVERandAQUA-DUCTanalyses to provide comprehensive insights into molecular details of transport processes related to biomolecules.Visit ourhomepage.OverviewUsing theTransportToolsengine, end-users can get access toefficient 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 tosimplify 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,TransportToolsengine can perform its action in 10 consecutive stages:Preparatory stage including defining transformations needed for unified analysesProcessing of input datasets of tunnel networksLayering tunnel clusters to get their simplified representationComputing distances among the layered clustersClustering the layered clusters into superclusters and creating initial outputsFiltering superclusters and creating filtered outputsProcessing datasets of transport events of ligandsLayering transport events to get their simplified representationAssigning transport events to tunnel networks in superclusters and creating initial outputsFiltering supercluster with events and creating filtered outputs with eventsNote that stages 7-10 depend on the availability of data on transport events from AQUA-DUCT and hence are optional.AvailabilityTransportToolsis licensed under:GNU GPL v3 license, and
the source code is available atgithub.com.InstallationTransportToolscan be installed either:via CONDA:if you do not have already, getconda management systemcreate new environment for transport tools:  conda create --name transport_tools python=3.8activate the environment: conda activate transport_toolsinstall TransportTools and all required dependencies: conda install transport_tools -c labbit -c conda-forgeor PyPi:pip install transport_toolsAdditionally, you might want to install following packages to enhance your experience usingTransportTools:AmberToolsto speed-up trajectory processing withpytrajengine; by following theseinstructionsPyMCubesto enable supercluster visualization with surface: pip install --upgrade PyMCubesMSMSto speed-up supercluster visualization with the surfaceTo start usingTransportToolstype:tt_engine.py --helpTroubleshootingIf you encounter any problems with installation, or the use ofTransportToolsplease contact us atgithub.com.DocumentationDocumentation can be found ongithub.com.ReferencesBrezovsky et al, 2022: TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them. Bioinformatics 38: 1752-1753Sequeiros-Borja et al, 2023: Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations, MethodsX 10C: 101968FundingThe initial development of this library was funded by the National Science Centre, Poland - grant no.2017/25/B/NZ1/01307and2017/26/E/NZ1/00548.