GilsonLabUCSD / pAPRikaLinks
Advanced toolkit for binding free energy calculations
☆33Updated last month
Alternatives and similar repositories for pAPRika
Users that are interested in pAPRika are comparing it to the libraries listed below
Sorting:
- RESP with inter- and intra-molecular constraints in Psi4.☆32Updated 2 years ago
- Package for consistent reporting of relative free energy results☆39Updated last week
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆33Updated 3 months ago
- Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.☆70Updated last month
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Updated 2 years ago
- Set up relative free energy calculations using a common scaffold☆24Updated last month
- Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits☆14Updated last week
- Best practice document for alchemical free energy calculations going to livecoms journal☆77Updated 2 weeks ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated 11 months ago
- Standalone charge assignment from Espaloma framework.☆40Updated last year
- ☆30Updated 2 months ago
- The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.☆12Updated 6 months ago
- An automated framework for generating optimized partial charges for molecules☆39Updated last month
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆28Updated 10 months ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆25Updated 5 years ago
- Algorithms for various Network Layouts and Tooling for planning FE Calculations☆19Updated 2 weeks ago
- ☆22Updated 3 years ago
- Comparison benchmarks between public force fields and Open Force Field Initiative force fields☆10Updated 2 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆34Updated last year
- ☆31Updated last year
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆60Updated last year
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆32Updated 4 months ago
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆72Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- This package contains tools for setting up hybrid-topology FE calculations☆31Updated 3 months ago
- ☆39Updated last year
- ☆44Updated 3 years ago
- Density based object completion over PBC.☆30Updated 9 months ago