gu-yaowen

hexo-theme-yilia

一个简洁优雅的hexo主题 A simple and elegant theme for hexo.

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

DiffDock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

graphein

Protein Graph Library

dgl-lifesci

Python package for graph neural networks in chemistry and biology

AlphaFold3

Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

AutoDock-Vina

AutoDock Vina

OpenHINE

An Open-Source Toolkit for Heterogeneous Information Network Embedding (HINE)

awesome-molecular-generation

Awesome papers related to generative molecular modeling and design.

NeuralPLexer

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

rdkit_summary

rdkit总结与实践

MoleculeACE

A tool for evaluating the predictive performance on activity cliff compounds of machine learning models

ConfGF

Implementation of Learning Gradient Fields for Molecular Conformation Generation (ICML 2021).

DiffBindFR

Diffusion model based protein-ligand flexible docking method

Rank-N-Contrast

[NeurIPS 2023, Spotlight] Rank-N-Contrast: Learning Continuous Representations for Regression

graph-representations

Comparing graph representations for molecular features prediction

Papyrus-scripts

MilGNet

MilGNet: Deep Multiple Instance Learning on Heterogeneous Graph for Drug-disease Association Prediction

comp-lab-class-2023

Computational Physical Chemistry Lab 2023

drug_discovery_perspective

MXtalTools

EquiVS

Employing Molecular Conformations for Ligand-based Virtual Screening with Equivariant Graph Neural Network and Deep Multiple Instance Learning

MGREL

gene disease prediction by ML

wzyFunc

this repository saves commonly used function for data preparation, statistic analysis and machine learning

PED_pred

Characteristics and waiting time prediction for patients in the pediatric emergency department

Stroke_PSN

PertKGE

Identifying compound-protein interactions with knowledge graph embedding of perturbation transcriptomics

Stroke_PSN