Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is probably one of the fastest FEP simulation with FREE GPU hardwares that the genearl public could have access to
☆28Sep 13, 2026Updated last week
Alternatives and similar repositories for NAMD-FEP
Users that are interested in NAMD-FEP are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- This script is designed for evaluating the binding affinity between a protein target and a small molecule, by calculating the binding fre…☆15May 1, 2023Updated 3 years 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
- MMTSB Tool Set☆33Jan 26, 2026Updated 7 months ago
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆31Jun 3, 2024Updated 2 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆24Jan 16, 2015Updated 11 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Clustering of SES virtual probes for pocket generation and ranking via Isolation Forest☆14Mar 22, 2023Updated 3 years ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Oct 27, 2022Updated 3 years ago
- ☆10May 17, 2021Updated 5 years ago
- Efficient Sampling of PROTAC-Induced Ternary Complexes☆20Jun 3, 2025Updated last year
- 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
- ☆23Jul 29, 2026Updated last month
- Set up relative free energy calculations using a common scaffold☆25Apr 21, 2026Updated 5 months ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆16Apr 3, 2026Updated 5 months ago
- A free energy command line tool using alchemlyb☆17Dec 11, 2022Updated 3 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A toolkit developed to predict and analyze PROTAC-mediated ternary complexes using AlphaFold3 and Boltz-1.☆45Jul 17, 2025Updated last year
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆77Aug 11, 2023Updated 3 years ago
- Scripts for running alchemical, free-energy perturbation simulations using Gromacs☆18Feb 27, 2018Updated 8 years ago
- Protein-Ligand Interaction Fingerprints☆21Dec 23, 2020Updated 5 years ago
- Tutorial to build AMBER compatable protein+lipid systems☆17Apr 19, 2017Updated 9 years ago
- ☆76Aug 13, 2026Updated last month
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆203Jul 6, 2023Updated 3 years ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆211Sep 22, 2023Updated 3 years ago
- Pocket dynamics analysis tool☆18Sep 9, 2026Updated 2 weeks ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ☆16Dec 24, 2016Updated 9 years ago
- ☆70Oct 11, 2022Updated 3 years ago
- The OpenMM Cookbook and Tutorials☆61Updated this week
- Automated Adaptive Absolute alchemical Free Energy calculator☆129Jul 28, 2026Updated last month
- Lightweight induced fit docking☆22May 22, 2023Updated 3 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Apr 27, 2023Updated 3 years ago
- pymol implementation of WaterDock with Akshay Sridhar (@akshay-sridhar) and refactoring work by Patrick McCubbin (@mccubbinp)☆11Mar 25, 2024Updated 2 years ago
- ☆23Aug 25, 2023Updated 3 years ago
- ☆85Dec 18, 2024Updated last year
- 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.
- Implementation of the Paper "iScore: A ML-Based Scoring Function for de novo Drug Discovery" by S.J. Mahdizadeh, and L.A. Eriksson.☆19Jun 26, 2026Updated 2 months ago
- Python Tools for NAMD☆25May 7, 2025Updated last year
- Learning Binding Affinities via Fine-tuning of Protein and Ligand Language Models☆40Aug 18, 2026Updated last month
- 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
- A toolkit to bulk-submission, download, analysis and summarizing data from abYsis.org☆10Apr 20, 2020Updated 6 years ago
- ☆58Jan 15, 2026Updated 8 months ago
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆20Aug 14, 2020Updated 6 years ago