Computation of the drug-target relative residence times from RAMD simulations
☆21Aug 29, 2024Updated last year
Alternatives and similar repositories for tauRAMD
Users that are interested in tauRAMD are comparing it to the libraries listed below
Sorting:
- Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.☆16Updated this week
- Code and datasets from the publication https://doi.org/10.1186/s13321-023-00787-9☆21Apr 21, 2024Updated last year
- Robust and stable clustering of molecular dynamics simulation trajectories.☆19Sep 2, 2022Updated 3 years ago
- Tutorial to build AMBER compatable protein+lipid systems☆16Apr 19, 2017Updated 8 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆43Jul 19, 2024Updated last year
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆24Jun 8, 2024Updated last year
- Tutorial using PLANTS (Protein-Ligand ANTSystem)☆13Jul 27, 2024Updated last year
- Bokeh extensions to plot molecules easily☆10Jul 14, 2025Updated 7 months ago
- Xlink is a Python script that uses Gromacs to automatically perfom simulation crosslinking and generate atomistic model of aromatic polya…☆16Jul 8, 2023Updated 2 years ago
- Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)☆14Jan 2, 2026Updated 2 months ago
- ☆13Apr 11, 2018Updated 7 years ago
- MD-ligand-receptor is a bioinformatics pipeline written in Python for analyzing non-covalent ligand-receptor interactions in 3D structure…☆10Jun 18, 2023Updated 2 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Feb 11, 2021Updated 5 years ago
- Fully automated high-throughput MD pipeline☆89Feb 13, 2026Updated 2 weeks ago
- Computational Chemistry Workflows☆56Jul 19, 2022Updated 3 years ago
- ☆26Jul 23, 2024Updated last year
- Demo of diffusion models #DDPM applied to molecular dynamics of small peptide☆14Jan 26, 2024Updated 2 years ago
- QM/MM Study Group☆15Jan 22, 2019Updated 7 years ago
- PyEMMA Jupyter Notebooks☆14Jan 28, 2021Updated 5 years ago
- Discontinuous Molecular Dynamics (DMD) Simulation Package☆15Mar 21, 2022Updated 3 years ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Mar 7, 2025Updated 11 months ago
- EC-Conf: An Ultra-fast Diffusion Model for Molecular conformation Generation with Equivariant Consistency☆12Mar 28, 2024Updated last year
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆18Sep 11, 2022Updated 3 years ago
- A Python library for constructing polymer topologies and coordinates☆18Sep 23, 2025Updated 5 months ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Feb 23, 2026Updated last week
- Automatic generation of LAMMPS data file for atomistic and coarse-grained simulations of molecular and polymeric materials with various t…☆17Feb 4, 2026Updated 3 weeks ago
- ☆16Jul 26, 2024Updated last year
- ☆15Jun 26, 2018Updated 7 years ago
- Predict allosteric pockets on proteins☆15Mar 28, 2022Updated 3 years ago
- Building and analyzing residue interaction networks with cofactors (includes tutorial).☆18Mar 31, 2021Updated 4 years ago
- ☆35Oct 14, 2024Updated last year
- Official implementation of RuSH (Scaffold Hopping with Generative Reinforcement Learning). Includes ScaffoldFinder algorithm for 2D decor…☆20Feb 20, 2025Updated last year
- ☆20Dec 15, 2025Updated 2 months ago
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆16Jan 20, 2022Updated 4 years ago
- Implementation of the Paper "iScore: A ML-Based Scoring Function for de novo Drug Discovery" by S.J. Mahdizadeh, and L.A. Eriksson (https…☆17Jun 14, 2024Updated last year
- Thompson Sampling☆78May 7, 2025Updated 9 months ago
- An implementation of the Solubility Forecast Index (SFI)☆24Oct 6, 2025Updated 4 months ago
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Mar 31, 2025Updated 11 months ago
- MDPath - A tool for calculating allosteric communication pathways in proteins by analyzing the mutual information of residue dihedral ang…☆28Feb 22, 2026Updated last week