This script is designed for evaluating the binding affinity between a protein target and a small molecule, by calculating the binding free energy, supporting both gmx and gmx_mpi, with or without GPU
☆16May 1, 2023Updated 3 years ago
Alternatives and similar repositories for Gromacs-ABF
Users that are interested in Gromacs-ABF are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Open Source, Prepare a molecular dynamic simulation from scratch without installing local VMD, use LigParGen for topology, it is one of t…☆14Jul 3, 2023Updated 3 years ago
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆29Oct 21, 2026Updated 2 weeks ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Dec 10, 2023Updated 2 years ago
- Alchemd is a Python-based CADD (Computer-Aided Drug Design) application specialized in free energy perturbation (FEP) calculations using …☆11May 26, 2026Updated 5 months ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆66Dec 17, 2025Updated 10 months ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Tutorial to build AMBER compatable protein+lipid systems☆17Apr 19, 2017Updated 9 years ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆17Apr 3, 2026Updated 7 months ago
- ☆10May 17, 2021Updated 5 years ago
- pymol implementation of WaterDock with Akshay Sridhar (@akshay-sridhar) and refactoring work by Patrick McCubbin (@mccubbinp)☆11Mar 25, 2024Updated 2 years ago
- A toolkit developed to predict and analyze PROTAC-mediated ternary complexes using AlphaFold3 and Boltz-1.☆45Jul 17, 2025Updated last year
- For the purpose of post progressing of MD carried by gromacs☆24Jul 2, 2025Updated last year
- Reference implementation of the COBDock algorithm.☆10Jul 9, 2024Updated 2 years ago
- 3D-MCTS: A general structure-based molecule generation method with MCTS.☆46Jun 26, 2024Updated 2 years ago
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆226Mar 4, 2026Updated 8 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Python code for generating Boresch restraints from MD simulations☆23Oct 11, 2025Updated last year
- Clustering of SES virtual probes for pocket generation and ranking via Isolation Forest☆14Mar 22, 2023Updated 3 years ago
- AutoGrow4 is an open-source program for semi-automated computer-aided drug discovery. It uses a genetic algorithm to evolve predicted lig…☆61Oct 7, 2025Updated last year
- Python module for identification of conserved water molecules from molecular dynamics trajectories.☆15Updated this week
- SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemb…☆18Jun 30, 2025Updated last year
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆58Apr 21, 2025Updated last year
- DualBind is a 3D structure-based deep learning model with a dual-loss framework for accurate and fast protein-ligand binding affinity pre…☆26Oct 21, 2025Updated last year
- Python code to run Supervised Molecular Dynamics (SuMD) simulations☆16Apr 24, 2024Updated 2 years ago
- Open Drug Discovery Toolkit (ODDT) Notebooks 101☆20Jun 22, 2018Updated 8 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Scripts for running alchemical, free-energy perturbation simulations using Gromacs☆18Feb 27, 2018Updated 8 years ago
- ☆19Jun 27, 2024Updated 2 years ago
- Automated Adaptive Absolute alchemical Free Energy calculator☆134Oct 5, 2026Updated last month
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆173Aug 18, 2026Updated 2 months ago
- ☆28Jul 3, 2024Updated 2 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆20Oct 29, 2026Updated last week
- Pocket dynamics analysis tool☆18Sep 9, 2026Updated last month
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆215Sep 22, 2023Updated 3 years ago
- Efficient Sampling of PROTAC-Induced Ternary Complexes☆20Jun 3, 2025Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein- Specific Molecular Generation☆23Jul 23, 2024Updated 2 years ago
- PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Comp…☆17Mar 18, 2026Updated 7 months ago
- Open-Sourced. Millions of small molecules will be downloaded from the ZINC database in 3D SDF file format, with one click, to get ready f…☆17Dec 29, 2023Updated 2 years ago
- Lightweight induced fit docking☆22May 22, 2023Updated 3 years ago
- A computational tool for the prediction and identification of metabolites.☆17Aug 19, 2021Updated 5 years ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆77Aug 11, 2023Updated 3 years ago
- Multiscale Simulation Tool for Backmapping☆22Mar 13, 2026Updated 7 months ago