deGrootLab / pmxLinks
Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
☆155Updated 2 weeks ago
Alternatives and similar repositories for pmx
Users that are interested in pmx are comparing it to the libraries listed below
Sorting:
- binding free energy estimator 2☆124Updated 3 months ago
- Benchmark set for relative free energy calculations.☆112Updated last year
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆190Updated last year
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆79Updated 2 years ago
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆143Updated 2 months ago
- Simple protein-ligand complex simulation with OpenMM☆87Updated last year
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆83Updated last month
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆208Updated 2 weeks ago
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆128Updated this week
- A python toolkit for analysing membrane protein-lipid interactions.☆64Updated 2 years ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆66Updated 2 years ago
- Describe and apply transformation on molecular structures and topologies☆118Updated last week
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆151Updated 5 months ago
- This repository contains notebooks for the workshop Python for Cheminformatics-Driven Molecular Docking held on May 1, 2025 in collaborat…☆83Updated 2 months ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆136Updated 2 weeks ago
- clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)☆116Updated last year
- The Free Energy Landscape Analysis tool offers a comprehensive suite for analyzing and visualizing the free energy landscape derived from…☆22Updated 6 months ago
- The public versio☆61Updated 2 years ago
- Scoring of shape and ESP similarity with RDKit☆222Updated last week
- An application for configuring and running simulations with OpenMM☆72Updated last month
- ☆76Updated 3 years ago
- Reduce - tool for adding and correcting hydrogens in PDB files☆151Updated 3 months ago
- ☆67Updated 2 years ago
- Auto3D generates low-energy conformers from SMILES/SDF☆177Updated 3 months ago
- Protein-Ligand Benchmark Dataset for Free Energy Calculations☆193Updated last year
- A tool for setting up free energy simulations.☆35Updated 2 years ago
- ☆56Updated 2 years ago
- An interoperable Python framework for biomolecular simulation.☆119Updated last week
- An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculatio…☆113Updated 9 months ago
- Modeling with limited data☆59Updated last month