☆25Aug 1, 2023Updated 2 years ago
Alternatives and similar repositories for AutoFEP_For_GMX
Users that are interested in AutoFEP_For_GMX are comparing it to the libraries listed below
Sorting:
- Adaptive string method implementation in AmberTools23 and Amber22☆14Jan 7, 2025Updated last year
- Entropy from PDB conformational ensembles☆13Mar 28, 2024Updated last year
- The official GitHub repository for the Nature Communications paper "Computational Design of Generalist Cyclopropanases with Stereodiverge…☆13Jan 23, 2026Updated last month
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆24Oct 18, 2019Updated 6 years ago
- Tools to add restraints to FEP runs. Includes a workflow to determine reference structures and restraint widths from plain MD simulations…☆11Jan 24, 2026Updated last month
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆206Sep 22, 2023Updated 2 years ago
- Various scripts for quantum chemistry (mainly ORCA)☆15Feb 6, 2025Updated last year
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆15Jun 15, 2019Updated 6 years ago
- A repository containing the build steps for the ccpbiosim workshop on QM/MM☆68Feb 27, 2026Updated last week
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆40Aug 11, 2023Updated 2 years ago
- The QED (Quantitative Estimation of Drug-likeness) molecular descriptor to use in combination with RDKit☆14Dec 12, 2022Updated 3 years ago
- ☆40Jul 17, 2024Updated last year
- A python package for computer-aid drug design.☆42Nov 21, 2025Updated 3 months ago
- The gmx_rrcs script is designed to calculate the residues-residues contact scores (rrcs) from a trajectory file generated by GROMACS.☆18Jun 16, 2025Updated 8 months ago
- Data visualizations for biomolecular dynamics☆17Oct 30, 2018Updated 7 years ago
- Structure-based self-supervised learning enables ultrafast prediction of stability changes upon mutations☆96Dec 10, 2025Updated 2 months ago
- EGDB: A Comprehensive Multi-Omics Database for Energy Grasses and the Epigenomic Atlas of Pearl Millet☆41Jan 30, 2025Updated last year
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆24Jun 8, 2024Updated last year
- Academic license pre-required. While FEP Plus charge you 100,000 USD per year. Here comes the FEP-Minus, it is a Schrodinger FEP Plus ide…☆24Jul 28, 2024Updated last year
- Rosetta Funclib☆25May 9, 2020Updated 5 years ago
- ☆21Dec 11, 2024Updated last year
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆59Apr 21, 2025Updated 10 months ago
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆135May 24, 2024Updated last year
- Trusted force field files for gromacs☆69Oct 31, 2024Updated last year
- 好的CADD教程，资源总结☆25Apr 8, 2024Updated last year
- FlexPose, a framework for AI-based flexible modeling of protein-ligand binding pose.☆55Dec 27, 2023Updated 2 years ago
- Automatic Fragment Linking with Deep Conditional Transformer Neural Networks☆55Feb 27, 2022Updated 4 years ago
- ☆20Oct 4, 2022Updated 3 years ago
- ☆31Dec 4, 2022Updated 3 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆67Apr 16, 2021Updated 4 years ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆35Dec 10, 2025Updated 2 months ago
- Fully automated high-throughput MD pipeline☆89Feb 13, 2026Updated 3 weeks ago
- ☆12Jul 30, 2019Updated 6 years ago
- ML-optimized library design with improved fitness and diversity for protein engineering☆36Nov 5, 2025Updated 4 months ago
- ☆37Aug 28, 2023Updated 2 years ago
- This software package simulates the reduction of graphene oxide and calculates the optical response of the generated sp2 domains☆11Dec 22, 2016Updated 9 years ago
- A tool for setting up free energy simulations.☆36Oct 20, 2022Updated 3 years ago
- Deciphering protein evolution and fitness landscapes with latent space models☆37Nov 2, 2021Updated 4 years ago
- ☆15Jun 29, 2015Updated 10 years ago