cai_yc's repositories
Atom-matching-network
Learning atom mappings in chemical reactions through deep graph matching
chemfiles
Library for reading and writing chemistry files
DECIMER.ai
This repository contains the code for https://decimer.ai
DiffDock
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
DiffLinker
DiffLinker: Equivariant 3D-Conditional Diffusion Model for Molecular Linker Design
DiffSBDD
A Euclidean diffusion model for structure-based drug design.
dockey
an integrated tool for molecular docking and virtual screening
dssp
Application to assign secondary structure to proteins
GaUDI
Guided Diffusion Model for Molecular Inverse Design
mdlib
MDLIB: Molecule Dynamics Library
Meeko
Interfacing RDKit and AutoDock
minGPT
A minimal PyTorch re-implementation of the OpenAI GPT (Generative Pretrained Transformer) training
molecular-complexity
Python implementation of the molecular complexity metric described by Proudfoot 2017 (http://dx.doi.org/10.1016/j.bmcl.2017.03.008).
moleculekit
MoleculeKit: Your favorite molecule manipulation kit
nanoGPT
The simplest, fastest repository for training/finetuning medium-sized GPTs.
openduck
Open-source DUck (Dynamic Undocking)
OpenMD
Molecular Dynamics in the Open
pandastable
Table analysis in Tkinter using pandas DataFrames.
pKa-ANI
Accurate prediction of protein pKa with representation learning
PyAutoFEP
PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
rDock
rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies.
reactiondataextractor2
This repo contains ReactionDataExtractor v.2 - software toolkit for extraction of information from chemical reaction schemes
ResGen
3D_Molecular_Generation
SurfGen
SurfGen: Learning on Topological Surface and Geometric Structure for 3D Molecular Generation
TinyGPT
Tiny C++11 GPT-2 inference implementation from scratch
torchmd
End-To-End Molecular Dynamics (MD) Engine using PyTorch
viamd
Visual Interactive Analysis of Molecular Dynamics