tubiana / TTClust
clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)
☆104Updated 4 months ago
Related projects: ⓘ
- binding free energy estimator 2☆101Updated last month
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆131Updated last month
- A python toolkit for analysing membrane protein-lipid interactions.☆58Updated last year
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆124Updated 6 months ago
- Benchmark set for relative free energy calculations.☆91Updated 3 months ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆73Updated last year
- Describe and apply transformation on molecular structures and topologies☆94Updated last week
- the simple alchemistry library☆191Updated this week
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆158Updated 11 months ago
- A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).☆56Updated last month
- some scripts for analysis of MD and CADD. And some tutorials.☆47Updated last month
- ☆47Updated last year
- Modeling with limited data☆54Updated 5 months ago
- Martini 3 small-molecule database☆54Updated 3 weeks ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆40Updated 3 years ago
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, com…☆166Updated this week
- LiveCoMS GROMACS Tutorials Paper☆105Updated 5 years ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆66Updated 3 months ago
- Auto3D generates low-energy conformers from SMILES/SDF☆146Updated last month
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆51Updated last year
- The Free Energy Landscape Analysis tool offers a comprehensive suite for analyzing and visualizing the free energy landscape derived from…☆12Updated last month
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆113Updated 3 months ago
- Force fields produced by the Open Force Field Initiative☆129Updated last week
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆113Updated last month
- MD trajectory analysis using protein-ligand Interaction Fingerprints☆59Updated 7 months ago
- Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse☆173Updated last month
- ☆38Updated 2 months ago
- ☆89Updated 2 years ago
- A Graph-Convolutional Deep Neural Network for predicting electrostatic potential surfaces☆85Updated last year
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆112Updated this week