Starred repositories
Full automation of relative protein-ligand binding free energy calculations in GROMACS
Protein-Ligand Benchmark Dataset for Free Energy Calculations
An open tool implementing some recommended practices for analyzing alchemical free energy calculations
Inputs, results, and pipeline code for Modular and Interoperable Workflows for Benchmarking Alchemical Binding Free Energy Calculation Methodologies manuscript.
A tutorials suite for BioSimSpace.
Topology Superimposition based on joint graph traversal
An interoperable Python framework for biomolecular simulation.
Automated Adaptive Absolute alchemical Free Energy calculator
PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RBFE) calculations on protein-ligand systems, compatible with …
OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method
Build coarse-grained mapping for molecules from a web-GUI
Tools for coarse-grained molecular dynamics simulations using the SPICA force field
Wrappers around NIST REFPROP for languages such as Python, MATLAB, etc.
Converters to go to/from other fluid file formats
teqp-based thermodynamic mixture model optimization
The python code for fitting interaction parameters for binary mixtures
GROMACS implementation of TraPPE-UA force field with HH-Alkane modifications
Python for chemoinformatics
Efficient and easy to use fortran implementation of the Ewald summation method
A Package for Parametrization of Molecular Mechanics Force Fields
Scripts for calculating RESP charges with Gaussian, starting only with .xyz file of your compound. Generate .mol2, .frcmod and .pdb with calculated RESP charges, for Molecular Dynamic simulations i…
Automated Backward and Forward Selection On Python
Tensorflow port of Image-to-Image Translation with Conditional Adversarial Nets https://phillipi.github.io/pix2pix/