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
☆29Nov 2, 2025Updated 4 months ago
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:
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Dec 10, 2023Updated 2 years ago
- This script is designed for evaluating the binding affinity between a protein target and a small molecule, by calculating the binding fre…☆14May 1, 2023Updated 2 years ago
- MMTSB Tool Set☆33Jan 26, 2026Updated 2 months ago
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆29Jun 3, 2024Updated last year
- Clustering of SES virtual probes for pocket generation and ranking via Isolation Forest☆14Mar 22, 2023Updated 3 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- Examples of applications of pymbar to various problems in simulation and experiment☆23Jan 16, 2015Updated 11 years ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆15Mar 11, 2026Updated 2 weeks 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
- Efficient Sampling of PROTAC-Induced Ternary Complexes☆12Jun 3, 2025Updated 9 months ago
- SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemb…☆18Jun 30, 2025Updated 8 months ago
- Automated Adaptive Absolute alchemical Free Energy calculator☆115Feb 9, 2026Updated last month
- ☆10May 17, 2021Updated 4 years ago
- Set up relative free energy calculations using a common scaffold☆24Aug 19, 2025Updated 7 months ago
- A free energy command line tool using alchemlyb☆17Dec 11, 2022Updated 3 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Tutorial to build AMBER compatable protein+lipid systems☆16Apr 19, 2017Updated 8 years ago
- Protein-Ligand Interaction Fingerprints☆21Dec 23, 2020Updated 5 years ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆74Aug 11, 2023Updated 2 years ago
- Scripts for running alchemical, free-energy perturbation simulations using Gromacs☆17Feb 27, 2018Updated 8 years ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆200Jul 6, 2023Updated 2 years ago
- Pocket dynamics analysis tool☆18May 8, 2025Updated 10 months ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆207Sep 22, 2023Updated 2 years ago
- ☆16Dec 24, 2016Updated 9 years ago
- Lightweight induced fit docking☆21May 22, 2023Updated 2 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Apr 27, 2023Updated 2 years ago
- A toolkit developed to predict and analyze PROTAC-mediated ternary complexes using AlphaFold3 and Boltz-1.☆41Jul 17, 2025Updated 8 months ago
- ☆65Oct 11, 2022Updated 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
- Implementation of the Paper "iScore: A ML-Based Scoring Function for de novo Drug Discovery" by S.J. Mahdizadeh, and L.A. Eriksson (https…☆17Jun 14, 2024Updated last year
- ☆22Aug 25, 2023Updated 2 years ago
- Python Tools for NAMD☆24May 7, 2025Updated 10 months ago
- Learning Binding Affinities via Fine-tuning of Protein and Ligand Language Models☆40Dec 5, 2024Updated last year
- ☆81Dec 18, 2024Updated last year
- NordVPN Threat Protection Pro™ • AdTake your cybersecurity to the next level. Block phishing, malware, trackers, and ads. Lightweight app that works with all browsers.
- Real time monitoring and visualization of Amber MD simulations☆16Feb 6, 2020Updated 6 years ago
- ☆46Jan 15, 2026Updated 2 months ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆158Mar 18, 2026Updated last week
- ☆72Feb 24, 2026Updated last month
- Some practical theoretic background needed for running MD simulations☆22Aug 1, 2025Updated 7 months ago
- A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS☆151Mar 19, 2026Updated last week
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Dec 4, 2024Updated last year