BioinfoMachineLearning

bio-diffusion

A geometry-complete diffusion generative model (GCDM) for 3D molecule generation and optimization. (Nature CommsChem)

PoseBench

Comprehensive benchmarking of protein-ligand structure prediction methods. (ICML 2024 AI4Science)

FlowDock

A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)

DIPS-Plus

The Enhanced Database of Interacting Protein Structures for Interface Prediction

GCPNet

A geometry-complete SE(3)-equivariant perceptron network (GCPNet) for 3D graphs. (Bioinformatics)

cryo2struct

The programs for preprocessing cryo-EM density maps for machine learning

CryoVirusDB

A dataset of labeled virus particles in cryo-EM micrographs (images) for training and testing machine learning methods of virus particle picking

GCDM-SBDD

A geometry-complete diffusion generative model (GCDM) for structure-based drug design (Nature CommsChem)

TransFew

Transformer for protein function prediction (version 2)

CDPred

Deep transformer for predicting interchain residue-residue distances of protein complexes

MULTICOM4

The MULTICOM4 protein structure prediction system developed by the Bioinformatics and Machine Learning Lab at the University of Missouri - Columbia

GRNformer

Transformer models for predicting gene regulatory networks from omics data

MULTICOM_ligand

Comprehensive ensembling of protein-ligand structure and affinity prediction methods (CASP16)

deep-learning-hpc-project-template

A PyTorch Lightning project template adapted for high-performance computing clusters such as Summit and Fugaku

GCPNet-EMA

Protein Structure Accuracy Estimation using Geometry-Complete Perceptron Networks (Protein Science 2024)

ScHiCEDRN

Single cell 3D genome modeling tools developed in the Bioinformatics and Machine Learning Lab

gate

Graph transformer for estimating protein model accuracy

hicdiff

Diffusion models for denoising Hi-C chromosome conformation capturing data

Cryo2Strut2

The second version of Cryo2Struct for reconstructing protein structures from cryo-EM density maps

denoisecryodata

The dataset for training machine learning methods to denoise cryo-EM density maps

HiCEGNN

A transformer method of reconstructing 3D structures of genomes and chromosomes from Hi-C data

PSBench

A large and comprehensive benchmark for estimating the accuracy of protein complex structural models

SERSFormer

Transformers for predicting food contamination

chai-lab

Chai-1, SOTA model for biomolecular structure prediction

mintomics

openfold-triton-evoformer

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

JCVIDB

A data repository for JCVI minimum cells

.github

DiffDock

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

tulip

Template-based modeling for accurate prediction of ligand-protein complex structures (TULIP)