Full automation of relative protein-ligand binding free energy calculations in GROMACS
☆47May 3, 2021Updated 5 years ago
Alternatives and similar repositories for ProtoCaller
Users that are interested in ProtoCaller are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆44Feb 15, 2022Updated 4 years ago
- Software for automated processing of alchemical free energy calculations☆12Nov 7, 2022Updated 3 years ago
- Code and resources for the EPSRC BioSimSpace project.☆78Sep 1, 2025Updated 11 months ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆82Jun 22, 2023Updated 3 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…☆225Mar 4, 2026Updated 5 months 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.
- Software tools for fragment-based drug discovery (FBDD)☆27Apr 6, 2020Updated 6 years ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆75Jun 12, 2023Updated 3 years ago
- Soft benchmark sets for alchemical free energy calculations, for assessing their accuracy on biomolecular systems☆18Mar 8, 2019Updated 7 years ago
- Galaxy Tools for Computational Chemistry☆16Mar 25, 2025Updated last year
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆211Sep 22, 2023Updated 2 years ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆203Jul 6, 2023Updated 3 years ago
- Molecular docking with Alchemical Interaction Grids☆32Nov 6, 2025Updated 9 months ago
- ☆24Jan 16, 2024Updated 2 years ago
- ☆31Jul 8, 2026Updated last month
- 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.
- Examples for use of YANK - getyank.org☆12Sep 20, 2021Updated 4 years ago
- A tool for setting up free energy simulations.☆37Oct 20, 2022Updated 3 years ago
- Scripts for running alchemical, free-energy perturbation simulations using Gromacs☆18Feb 27, 2018Updated 8 years ago
- gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.☆324Jul 31, 2026Updated last week
- ☆25Oct 30, 2020Updated 5 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 7 years ago
- HIPPOS Is PyPLIF On Steroids. A Molecular Interaction Fingerprinting Tool for Docking Results of Autodock Vina and PLANTS☆32Aug 15, 2023Updated 2 years ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆31Dec 19, 2021Updated 4 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆181Jul 28, 2026Updated last week
- 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.
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆76Jun 30, 2026Updated last month
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Dec 10, 2023Updated 2 years ago
- Source code and input files associated to the paper "Targeted free energy perturbation revisited: Accurate free energies from mapped refe…☆13Sep 14, 2021Updated 4 years ago
- ☆22Aug 30, 2022Updated 3 years ago
- Unified Free Energy Dynamics (UFED) simulations with OpenMM☆37Aug 20, 2025Updated 11 months ago
- ☆16Dec 24, 2016Updated 9 years ago
- Optimization of binding affinities in chemical space for drug discovery☆36Jan 31, 2023Updated 3 years ago
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆140May 24, 2024Updated 2 years ago
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆20Aug 14, 2020Updated 5 years 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.
- Benchmark set for relative free energy calculations.☆121May 22, 2024Updated 2 years ago
- RF-Score-VS binary☆33Nov 18, 2018Updated 7 years ago
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆144Nov 10, 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 last year
- Molecular Property Prediction using GP with a SOAP kernel☆22Nov 16, 2020Updated 5 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Apr 7, 2022Updated 4 years ago
- De novo molecular design with deep molecular generative models for protein-protein interaction(PPI) inhibitors☆22Nov 6, 2024Updated last year