alchemistry / alchemical-best-practices
Best practice document for alchemical free energy calculations going to livecoms journal
☆69Updated last month
Alternatives and similar repositories for alchemical-best-practices:
Users that are interested in alchemical-best-practices are comparing it to the libraries listed below
- ☆43Updated 3 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated last year
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆33Updated last week
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆66Updated 2 weeks ago
- Given an RDKit molecule that does not sanitise, correct it until it does☆39Updated 11 months ago
- ☆53Updated last year
- Materials from the (virtual) 2020 RDKit UGM☆52Updated 4 years ago
- 📐 Symmetry-corrected RMSD in Python☆93Updated this week
- Advanced toolkit for binding free energy calculations☆32Updated 2 months ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆43Updated 3 years ago
- Experimental small molecule hydration free energy dataset☆30Updated 3 years ago
- Ensembler is a python package that provides fast and easy access to 1D and 2D model system simulations. It can be used for method develop…☆53Updated 11 months ago
- Accurate prediction of protein pKa with representation learning☆42Updated last month
- Package for consistent reporting of relative free energy results☆39Updated this week
- ☆21Updated 2 years ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆66Updated last year
- ☆33Updated 6 months ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆78Updated 9 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆58Updated last year
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆123Updated 2 weeks ago
- ☆64Updated last year
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium☆36Updated 2 weeks ago
- Standalone charge assignment from Espaloma framework.☆39Updated 8 months ago
- Sire Molecular Simulations Framework☆48Updated last week
- A tool for setting up free energy simulations.☆35Updated 2 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 2 years ago
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆28Updated 6 months ago
- Set up relative free energy calculations using a common scaffold☆22Updated 7 months ago