a VMD plugin for binding affinity prediction using end-point free energy methods
☆28Apr 23, 2016Updated 9 years ago
Alternatives and similar repositories for CaFE_Plugin
Users that are interested in CaFE_Plugin are comparing it to the libraries listed below
Sorting:
- Robust and stable clustering of molecular dynamics simulation trajectories.☆19Sep 2, 2022Updated 3 years ago
- MM/PBSA binding free energy calculation☆22May 31, 2024Updated last year
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆61Dec 17, 2025Updated 2 months ago
- iPBSA minimizes docked receptor-ligand conformations in implicit solvent and calculates the binding free energy with MM/PB(GB)SA methods.…☆13Oct 10, 2023Updated 2 years ago
- MDverse web scrapper 🔎🔧📄☆15Feb 21, 2026Updated last week
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆18Sep 11, 2022Updated 3 years ago
- 3D ligand-based pharmacophore modeling☆53Jan 12, 2026Updated last month
- ASGARD is a tool that allows via an automated MD workflow to perform MD protein or protein-ligand complex analysis and to generate the co…☆18Jul 11, 2024Updated last year
- A simplified drug discovery pipeline -- generating SMILE molecular with AlphaSMILES, predicting protein structure with AlphaFold, and che…☆18Aug 13, 2021Updated 4 years ago
- Multiscale Simulation Tool for Backmapping☆22Feb 7, 2026Updated 2 weeks ago
- a tool for protein-ligand binding affinity prediction☆37Mar 12, 2023Updated 2 years ago
- ☆12Jul 30, 2019Updated 6 years ago
- development repository for PyInteraph2☆22Mar 26, 2025Updated 11 months ago
- scripts for analyzing molecular dynamics trajectories using VMD☆39May 28, 2015Updated 10 years ago
- ☆10Nov 23, 2018Updated 7 years ago
- App for serotonergic targets☆12Jan 8, 2026Updated last month
- Public version for DistPepFold☆10Jul 17, 2025Updated 7 months ago
- Visual Molecular Dynamics in Docker Container☆12Jan 1, 2015Updated 11 years ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆93Jul 16, 2025Updated 7 months ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆169Feb 12, 2026Updated 2 weeks ago
- A Python package to calculate, visualize and analyze correlation maps of proteins.☆44Sep 3, 2025Updated 5 months ago
- ☆21Dec 11, 2024Updated last year
- Cryptic pocket prediction using AlphaFold 2☆24Nov 27, 2022Updated 3 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆74Jan 30, 2026Updated 3 weeks ago
- Example files for Colvars module: https://github.com/Colvars/colvars☆13Dec 7, 2021Updated 4 years ago
- Tool suite for analysing molecular dynamics trajectories using network analysis and PRS☆53May 30, 2025Updated 9 months ago
- Fast and versatile biomolecular structure PDB file parser using SQL queries☆24Mar 17, 2023Updated 2 years ago
- Protein surface topographical mapping tool☆29Aug 17, 2023Updated 2 years ago
- Open-source protein-based pharmacophore modeling software☆36Feb 15, 2025Updated last year
- A package to draw custom heatmaps on molecular depictions of RDKit☆13Mar 31, 2022Updated 3 years ago
- Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.☆15Sep 20, 2018Updated 7 years ago
- Clustering tool for biomolecular structural ensembles and data in general.☆10Aug 24, 2020Updated 5 years ago
- Python package wrapping the DOCK Fortran program and providing several tools built on top of it.☆15Jan 16, 2026Updated last month
- A distance distribution-based visualization method for atomic pair energy and precise prediction of absolute binding free energy.☆15Feb 4, 2025Updated last year
- Accelerated sampling framework with autoencoder-based method☆23Sep 7, 2019Updated 6 years ago
- Open Drug Metabolism & PharmacoKinetics (OpenDMPK) is an open source data resource and toolkit for predicting drug metabolism and pharmac…☆26Dec 31, 2021Updated 4 years ago
- Collection of scripts that integrates docking, virtual screening, similarity and molecular modeling programs.☆30Dec 16, 2025Updated 2 months ago
- Yasara plugins for Gromacs users☆33Jan 8, 2024Updated 2 years ago
- A Rust implementation of the LightDock macromolecular docking software☆30Apr 19, 2024Updated last year