Python code for generating Boresch restraints from MD simulations
☆23Oct 11, 2025Updated 8 months ago
Alternatives and similar repositories for MDRestraintsGenerator
Users that are interested in MDRestraintsGenerator are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- 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
- Data set of protein-ligand complexes with reliable experimental structures and affinities☆46Oct 2, 2025Updated 9 months ago
- Materials for the 2021 PRACE Workshop @ SurfSARA☆30Nov 11, 2021Updated 4 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆29Dec 4, 2024Updated last year
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Jan 3, 2026Updated 6 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- This script is designed for evaluating the binding affinity between a protein target and a small molecule, by calculating the binding fre…☆15May 1, 2023Updated 3 years 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
- Repository for the 2024 OpenFE industry benchmark efforts☆42Oct 3, 2025Updated 9 months ago
- Standalone charge assignment from Espaloma framework.☆47Oct 10, 2025Updated 8 months ago
- ☆17Jul 28, 2022Updated 3 years ago
- A free energy command line tool using alchemlyb☆17Dec 11, 2022Updated 3 years ago
- ☆29Feb 27, 2026Updated 4 months ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆74Jun 12, 2023Updated 3 years ago
- ☆21Jun 2, 2026Updated last month
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ☆12Jul 31, 2020Updated 5 years ago
- Alchemical mutation scoring map☆43Updated this week
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆16Apr 3, 2026Updated 3 months ago
- Plugins to enable using custom functional forms in SMIRNOFF based force fields☆11Jun 22, 2026Updated last week
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆79Jun 19, 2026Updated 2 weeks ago
- TorchMD-NET. This is a simple code to train Schnet using pytorch-lighthing.☆11Nov 10, 2021Updated 4 years ago
- Spectral Gap Optimization of Parameters☆18Mar 28, 2020Updated 6 years ago
- Benchmarking active learning protocols for ligand binding affinity prediction☆13Feb 4, 2024Updated 2 years ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆68Mar 29, 2026Updated 3 months 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.
- 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
- 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 6 months ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆178Mar 11, 2026Updated 3 months ago
- RESP with inter- and intra-molecular constraints in Psi4.☆32May 26, 2023Updated 3 years ago
- programs and scripts for molecular structure analysis☆12Mar 26, 2026Updated 3 months ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated last year
- Package for consistent reporting of relative free energy results☆42Jun 17, 2026Updated 2 weeks ago
- ☆16Dec 24, 2016Updated 9 years ago
- Supporting data for the manuscript "Deep learning the slow modes for rare events sampling"☆23Jun 6, 2024Updated 2 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.
- ☆37Nov 9, 2023Updated 2 years ago
- Learning Binding Affinities via Fine-tuning of Protein and Ligand Language Models☆40Mar 30, 2026Updated 3 months ago
- Open-source docking pipeline leveraging pairwise statistics☆15Jul 26, 2024Updated last year
- Identifying silly molecules☆17May 12, 2022Updated 4 years ago
- protein structure prediction with precision☆29May 14, 2024Updated 2 years ago
- ☆23Aug 25, 2023Updated 2 years ago
- ☆14Sep 18, 2023Updated 2 years ago