Sire Molecular Simulations Framework
☆64Feb 18, 2026Updated last week
Alternatives and similar repositories for sire
Users that are interested in sire are comparing it to the libraries listed below
Sorting:
- An interoperable Python framework for biomolecular simulation.☆146Updated this week
- Automated Adaptive Absolute alchemical Free Energy calculator☆114Feb 9, 2026Updated 2 weeks ago
- A tutorials suite for BioSimSpace.☆34Oct 22, 2025Updated 4 months ago
- ☆45Sep 5, 2024Updated last year
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆72Feb 13, 2026Updated 2 weeks ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Sep 27, 2023Updated 2 years ago
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆64Feb 9, 2026Updated 2 weeks ago
- Code and resources for the EPSRC BioSimSpace project.☆78Sep 1, 2025Updated 5 months ago
- Force fields produced by the Open Force Field Initiative☆179Jan 13, 2026Updated last month
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆154Feb 17, 2026Updated last week
- An engine for electrostatic ML embedding for multiscale modelling.☆26Feb 20, 2026Updated last week
- DFMDock (Denoising Force Matching Dock), a diffusion model that unifies sampling and ranking within a single framework.☆53Jul 22, 2025Updated 7 months ago
- ☆18Jul 29, 2025Updated 7 months ago
- A comprehensive toolkit for predicting free energies☆58Jan 10, 2025Updated last year
- Sire Molecular Simulations Framework☆97Jul 17, 2023Updated 2 years ago
- Protein-Ligand Benchmark Dataset for Free Energy Calculations☆216Jul 29, 2024Updated last year
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆83Jan 8, 2025Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Dec 10, 2023Updated 2 years ago
- A package for all physics based/related models☆54Sep 12, 2024Updated last year
- Python implementation of the multistate Bennett acceptance ratio (MBAR)☆292Feb 12, 2026Updated 2 weeks ago
- A simple implementation of replica exchange MD simulations for OpenMM.☆24Jul 19, 2021Updated 4 years ago
- An automated framework for generating optimized partial charges for molecules☆40Feb 18, 2026Updated last week
- moldrug (AKA mouse) is a Python package for drug-oriented optimization on the chemical space ☆39Nov 5, 2025Updated 3 months ago
- Material for the 3rd i-CoMSE Workshop: Methods for Advanced Sampling☆42May 1, 2023Updated 2 years ago
- The Open Free Energy toolkit☆253Updated this week
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆140Nov 10, 2025Updated 3 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.☆61Dec 17, 2025Updated 2 months ago
- The source code for ADME@NCATS application that hosts prediction models for ADME properties. Link to application: https://opendata.ncats.…☆39Feb 20, 2026Updated last week
- Dock organometallic compounds to proteins/DNA/biomolecules☆19May 26, 2025Updated 9 months ago
- Flexible Artificial Intelligence Docking☆17Aug 27, 2025Updated 6 months ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆169Feb 12, 2026Updated 2 weeks ago
- Simple package for fast molecular similarity searches☆164Updated this week
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆350Jan 6, 2026Updated last month
- Colab version of "DiffDock: : Diffusion Steps, Twists, and Turns for Molecular Docking"☆26Nov 12, 2022Updated 3 years ago
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆315Jan 7, 2026Updated last month
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆220Jan 27, 2026Updated last month
- Flexible storage of chemical topology for molecular simulation☆68Feb 17, 2026Updated last week
- Zero Shot Molecular Generation via Similarity Kernels☆28Aug 27, 2025Updated 6 months ago
- ☆25Jan 16, 2024Updated 2 years ago