Truman Xu's repositories
RxnEnumeration
Reaction Enumeration Using rdkit
hgraph2graph
Hierarchical Generation of Molecular Graphs using Structural Motifs
ArgonSim
Verlet's Argon simulation using numpy
AutoDock-Vina
AutoDock Vina
biopython
Fork of Biopython for CHARMM integration
charmm-script-vscode-extension
VS Code extension for CHARMM script syntax highlighting
chemutils
Utility function and scripts for chem routines
faerun-python
A python module for generating interactive views of chemical spaces.
CpHMD-Prep
Structure Preparation Routine for Constant Ph MD Simulation using crimm
DiffDock
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
FastJTNNpy3
AI for discovering 100% valid drug like molecules, a combination of VAE-JTNN and bayesian optimization, an optimized Python 3 Version of Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)
jtvae
Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)
openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
pdb2pqr-charmm
PDB2PQR - Fork for a better integration with CHARMM
pdbtbx
A library to open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files in Rust.
pyCHARMM-Workshop
This repository contains materials for the pyCHARMM Workshop run at the University of Michigan by Charles Brooks' Group, June 20-24
RNAPosers
A Set of Machine Learning Classifiers For RNA Containing Complexes
SampleDock
Molecular design framework the merges generative AI and molecular docking
TF3P
Three-dimensional force fields fingerprints
toolset
MMTSB Tool Set