Chemoinformatics tools
Institute of Molecular and Translational Medicine, Palacky University
StreaMD - fully automatic distributed molecular dynamic pipeline using GROMACS
The open-source software to simulate different molecular systems and analyze the output.
Features:
- supports run of multiple simultaneous molecular dynamics simulations
- supports simulation for different systems:
- Protein in Water
- Protein - Ligand
- Protein - Cofactor (multiple)
- Protein - Ligand - Cofactor (multiple)
- supports of simulations of boron-containing molecules using Gaussian Software
- supports of simulations of ligand binding metalloproteins with MCPB.py
- supports distributed computing using dask library
- supports of running of parallel simulations on multiple servers
- supports to extend time of MD simulations
- supports to continue of interrupted MD simulation
- interrupted MD preparation can be restarted by invoking the same command
- implemented tools for end-state free energy calculations (gmx_MMPBSA) and Protein-Ligand Interaction analysis (ProLIF)
Repository:
https://github.com/ci-lab-cz/streamdCitation:
Ivanova, A.; Mokshyna, O.; Polishchuk, P. StreaMD: the toolkit for high-throughput molecular dynamics simulations. J. Cheminf. 2024, 16 (1), 123. - https://doi.org/10.1186/s13321-024-00918-w