molmod / openmm-tutorial-msbs
OpenMM tutorial for the MSBS course
☆147Updated this week
Related projects ⓘ
Alternatives and complementary repositories for openmm-tutorial-msbs
- the simple alchemistry library☆199Updated last week
- ☆123Updated 7 months ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆137Updated 3 months ago
- Force fields produced by the Open Force Field Initiative☆140Updated last week
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆130Updated last week
- Describe and apply transformation on molecular structures and topologies☆99Updated this week
- binding free energy estimator 2☆108Updated 2 weeks ago
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆178Updated last month
- OFFICIAL: AnteChamber PYthon Parser interfacE☆206Updated 2 months ago
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆119Updated 6 months ago
- Auto3D generates low-energy conformers from SMILES/SDF☆149Updated 3 months ago
- Scoring of shape and ESP similarity with RDKit☆206Updated last year
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆259Updated last week
- ☆89Updated 2 years ago
- Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse☆181Updated last week
- Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196☆215Updated this week
- Benchmark set for relative free energy calculations.☆99Updated 6 months ago
- Protein-Ligand Benchmark Dataset for Free Energy Calculations☆150Updated 3 months ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆181Updated last year
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆165Updated last year
- A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …☆109Updated 5 years ago
- Simple protein-ligand complex simulation with OpenMM☆73Updated last year
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆120Updated 3 weeks ago
- ☆49Updated last year
- CReM: chemically reasonable mutations framework☆209Updated this week
- Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates☆128Updated last month
- ☆64Updated 10 months ago
- Python implementation of the multistate Bennett acceptance ratio (MBAR)☆240Updated last month
- LiveCoMS GROMACS Tutorials Paper☆109Updated 5 years ago
- Interface for AutoDock, molecule parameterization☆205Updated this week