JoaoRodrigues / gmx-toolsLinks
Assorted Python Scripts to accompany the gmx analysis tools
☆12Updated 6 years ago
Alternatives and similar repositories for gmx-tools
Users that are interested in gmx-tools are comparing it to the libraries listed below
Sorting:
- This repository contains notebooks for the workshop Python for Cheminformatics-Driven Molecular Docking held on May 1, 2025 in collaborat…☆82Updated last month
- Describe and apply transformation on molecular structures and topologies☆116Updated last week
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆150Updated 4 months ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆62Updated 4 years ago
- Input files for GROMACS tutorials written for the Journal of Physical Chemistry B☆20Updated 11 months ago
- Open-source tool to generate 3D-ready small molecules for virtual screening☆58Updated last week
- Simple protein-ligand complex simulation with OpenMM☆85Updated last year
- binding free energy estimator 2☆121Updated last month
- Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation☆122Updated last year
- CHAPERONg: An automated pipeline for GROMACS MD simulations and trajectory analyses☆49Updated 6 months ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆61Updated last year
- INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems☆65Updated last year
- Ligand-Protein Interaction Mapping☆56Updated 2 months ago
- ☆65Updated 2 years ago
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆140Updated last month
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆83Updated 3 weeks ago
- Adds or removes hydrogen atoms to achieve the appropriate molecular protonation state for a user-specified pH range☆34Updated 2 weeks ago
- A python toolkit for analysing membrane protein-lipid interactions.☆63Updated 2 years ago
- A python module to plot secondary structure schemes☆25Updated last year
- PandaDock: A Physics-Based Molecular Docking using Python☆70Updated this week
- Material from papers from KULL centre☆69Updated last year
- The Free Energy Landscape Analysis tool offers a comprehensive suite for analyzing and visualizing the free energy landscape derived from…☆22Updated 5 months ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆77Updated 2 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆151Updated last week
- FreeSASA Python Module☆55Updated last year
- An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculatio…☆112Updated 8 months ago
- BitBIRCH clustering algorithm☆89Updated last month
- Python package to run molecular dynamics simulation of a protein-ligand complex in a single line of code.☆146Updated this week
- Implementations of different GNNs from scratch for chemists☆139Updated last month
- The public versio☆59Updated 2 years ago