Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertubation with OpenMM.

Open-sourced. A cloud-based workflow to evaluate the confidence of a given docked pose with binding pose metadynamics

Protein Graph Library

The Database Toolkit for Python

My first ever repository, some notebooks useful, others sucks. Topics include file format conversion with obabel, docking with Auto Dock, MD with Charmm GUI and QSAR etc, never expect the format is…

A python script for PyMol to make protein-ligand interaction images.

Cloud-based molecular simulations for everyone

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

ArchLinux based WSL Distribution. Supports multiple install.

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

raster3d mirror/archive from http://www.bmsc.washington.edu/raster3d/

Free monospaced font with programming ligatures