Simple protein-ligand complex simulation with OpenMM
☆95Sep 6, 2023Updated 2 years ago
Alternatives and similar repositories for simple-simulate-complex
Users that are interested in simple-simulate-complex are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆175May 22, 2026Updated 2 months 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
- OpenMM tutorial for the MSBS course☆195Mar 19, 2026Updated 4 months ago
- Automated Adaptive Absolute alchemical Free Energy calculator☆123Jul 28, 2026Updated 2 weeks ago
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆378Aug 5, 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.
- A command line application to launch molecular dynamics simulations with OpenMM☆40Apr 7, 2022Updated 4 years ago
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆336Jan 7, 2026Updated 7 months ago
- An application for configuring and running simulations with OpenMM☆83Oct 30, 2025Updated 9 months ago
- The Open Free Energy toolkit☆319Updated this week
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆173Aug 2, 2026Updated last week
- ☆72Feb 13, 2026Updated 6 months ago
- ☆50Sep 5, 2024Updated last year
- Notebooks demonstrating how to do simple tasks related to free energy calculations.☆68Jul 7, 2026Updated last month
- Cloud-based Drug Binding Structure Prediction☆48Jul 13, 2026Updated last month
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- An open library to work with pharmacophores.☆51Jul 6, 2023Updated 3 years ago
- Benchmark set for relative free energy calculations.☆121May 22, 2024Updated 2 years ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆211Sep 22, 2023Updated 2 years ago
- ☆101Feb 24, 2025Updated last year
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆65Dec 17, 2025Updated 7 months ago
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 5 years ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆82Jun 22, 2023Updated 3 years ago
- ☆36Jun 17, 2026Updated last month
- SST2 implementation in openmm☆23Jul 9, 2026Updated last month
- 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.
- Scoring of shape and ESP similarity with RDKit☆236Aug 19, 2025Updated 11 months ago
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆31Jun 3, 2024Updated 2 years ago
- ☆27Jun 30, 2026Updated last month
- 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
- ☆40Feb 20, 2026Updated 5 months ago
- Fully automated high-throughput MD pipeline☆105Jul 23, 2026Updated 3 weeks ago
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆203Jul 6, 2023Updated 3 years ago
- Interaction Fingerprints for protein-ligand complexes and more☆530Aug 1, 2026Updated last week
- A toolkit developed to predict and analyze PROTAC-mediated ternary complexes using AlphaFold3 and Boltz-1.☆44Jul 17, 2025Updated last year
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse☆207Jun 28, 2026Updated last month
- OpenMM plugin to interface with PLUMED☆82Jan 15, 2026Updated 6 months ago
- Protein-ligand structure prediction☆241Jul 31, 2025Updated last year
- PDBFixer fixes problems in PDB files☆668Mar 10, 2026Updated 5 months ago
- Auto3D generates low-energy conformers from SMILES/SDF☆195Updated this week
- repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model☆302Dec 23, 2025Updated 7 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆38Sep 16, 2025Updated 10 months ago