A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
☆16Apr 3, 2026Updated 3 months ago
Alternatives and similar repositories for SAFEP_tutorial
Users that are interested in SAFEP_tutorial 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 repository contained python code used to do organic free energy calculation. Reference: http://www.bevanlab.biochem.vt.edu/Pages/Per…☆11Aug 2, 2018Updated 7 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆76Jun 30, 2026Updated 2 weeks ago
- Tautomer ratios in solution☆28Sep 20, 2021Updated 4 years ago
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆20Aug 14, 2020Updated 5 years ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated last year
- 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.
- ☆10May 17, 2021Updated 5 years ago
- ☆23Aug 25, 2023Updated 2 years ago
- EnzyDock: Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes☆18Sep 5, 2024Updated last year
- Python optimisation of atomistic ligand charges to maximize receptor binding affinity☆12Aug 3, 2020Updated 5 years ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆171Jun 5, 2026Updated last month
- Some practical theoretic background needed for running MD simulations☆22Jun 2, 2026Updated last month
- Software package for FEP☆23Mar 3, 2026Updated 4 months ago
- ☆13Jul 11, 2026Updated last week
- Examples for use of YANK - getyank.org☆12Sep 20, 2021Updated 4 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆22May 14, 2025Updated last year
- MMTSB Tool Set☆33Jan 26, 2026Updated 5 months ago
- Set up relative free energy calculations using a common scaffold☆24Apr 21, 2026Updated 2 months ago
- PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Comp…☆17Mar 18, 2026Updated 4 months ago
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆29Nov 2, 2025Updated 8 months ago
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆34Jun 3, 2025Updated last year
- ☆90Jul 19, 2023Updated 3 years ago
- Fast PBC wrapping and unwrapping for VMD☆27Nov 25, 2024Updated last year
- Bayesian Multistate Bennett Acceptance Ratio Method☆16Jun 28, 2026Updated 3 weeks 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.
- A free energy command line tool using alchemlyb☆17Dec 11, 2022Updated 3 years ago
- Automated Adaptive Absolute alchemical Free Energy calculator☆123May 1, 2026Updated 2 months ago
- This package contains tools for setting up hybrid-topology FE calculations☆38Updated this week
- Alchemical mutation scoring map☆45Jul 7, 2026Updated last week
- A tool for setting up free energy simulations.☆37Oct 20, 2022Updated 3 years ago
- ☆14Sep 18, 2023Updated 2 years ago
- ☆18May 11, 2026Updated 2 months ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆87Jan 8, 2025Updated last year
- ☆28Jan 9, 2024Updated 2 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.
- Python based Graphical User Interface for generating input files for and running molecular dynamic simulation.☆10Aug 27, 2024Updated last year
- ☆17Jul 28, 2022Updated 3 years ago
- Benchmarking active learning protocols for ligand binding affinity prediction☆13Feb 4, 2024Updated 2 years ago
- Hackable AlphaFold 3 inference pipeline.☆35Jun 18, 2025Updated last year
- binding free energy estimator 2☆144Updated this week
- The OpenMM Cookbook and Tutorials☆58Apr 28, 2026Updated 2 months ago
- High level API for using machine learning models in OpenMM simulations☆176Updated this week