BioinfoMachineLearning

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45 repositories

PoseBench
Public
Comprehensive benchmarking of protein-ligand structure prediction methods. (ICML 2024 AI4Science)
benchmark machine-learning deep-learning computational-biology computational-chemistry structure-prediction molecular-docking
Jupyter Notebook
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MIT License
•6•161•1•0•Updated Jul 30, 2025Jul 30, 2025
PSBench
Public
A large and comprehensive benchmark for estimating the accuracy of protein complex structural models
C
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MIT License
•0•0•0•0•Updated Jul 27, 2025Jul 27, 2025
GRNformer
Public
Transformer models for predicting gene regulatory networks from omics data
Python
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MIT License
•1•7•0•0•Updated Jul 7, 2025Jul 7, 2025
denoisecryodata
Public
The dataset for training machine learning methods to denoise cryo-EM density maps
Python
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MIT License
•0•2•1•0•Updated Jul 5, 2025Jul 5, 2025
MULTICOM4
Public
The MULTICOM4 protein structure prediction system developed by the Bioinformatics and Machine Learning Lab at the University of Missouri - Columbia
Python
•3•8•0•0•Updated Jun 28, 2025Jun 28, 2025
gate
Public
Graph transformer for estimating protein model accuracy
C
•1•3•0•0•Updated Jun 24, 2025Jun 24, 2025
.github
Public
0•0•0•0•Updated Jun 12, 2025Jun 12, 2025
mintomics
Public
Python
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MIT License
•1•1•0•0•Updated Jun 2, 2025Jun 2, 2025
bio-diffusion
Public
A geometry-complete diffusion generative model (GCDM) for 3D molecule generation and optimization. (Nature CommsChem)
machine-learning deep-learning computational-biology computational-chemistry generative-model graph-neural-networks
Python
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Other
•28•212•1•0•Updated May 30, 2025May 30, 2025
GCPNet
Public
A geometry-complete SE(3)-equivariant perceptron network (GCPNet) for 3D graphs. (Bioinformatics)
machine-learning deep-learning computational-biology graph-neural-networks
Python
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MIT License
•5•47•0•0•Updated Apr 20, 2025Apr 20, 2025
chai-lab
Public
Chai-1, SOTA model for biomolecular structure prediction
Python
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Apache License 2.0
•235•1•0•0•Updated Apr 15, 2025Apr 15, 2025
FlowDock
Public
A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)
machine-learning deep-learning computational-biology computational-chemistry generative-model structure-prediction molecular-docking
Python
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MIT License
•15•96•1•0•Updated Apr 7, 2025Apr 7, 2025
deep-learning-hpc-project-template
Public
A PyTorch Lightning project template adapted for high-performance computing clusters such as Summit and Fugaku
Python
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Apache License 2.0
•2•6•0•1•Updated Mar 21, 2025Mar 21, 2025
MULTICOM_ligand
Public
Comprehensive ensembling of protein-ligand structure and affinity prediction methods (CASP16)
deep-learning drug-discovery protein-ligand-interactions diffusion-model binding-affinity pose-prediction flow-matching
Jupyter Notebook
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MIT License
•0•7•0•0•Updated Mar 19, 2025Mar 19, 2025
openfold-triton-evoformer
Public
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
Python
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Apache License 2.0
•616•1•0•0•Updated Mar 13, 2025Mar 13, 2025
Cryo2Strut2
Public
The second version of Cryo2Struct for reconstructing protein structures from cryo-EM density maps
Python
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MIT License
•0•3•0•0•Updated Feb 18, 2025Feb 18, 2025
hicdiff
Public
Diffusion models for denoising Hi-C chromosome conformation capturing data
Python
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MIT License
•0•4•2•0•Updated Jan 21, 2025Jan 21, 2025
TransFew
Public
Transformer for protein function prediction (version 2)
Jupyter Notebook
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MIT License
•0•14•1•0•Updated Dec 20, 2024Dec 20, 2024
GCDM-SBDD
Public
A geometry-complete diffusion generative model (GCDM) for structure-based drug design (Nature CommsChem)
Python
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MIT License
•5•19•0•0•Updated Nov 6, 2024Nov 6, 2024
cryo2struct
Public
The programs for preprocessing cryo-EM density maps for machine learning
Python
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MIT License
•2•29•0•0•Updated Oct 1, 2024Oct 1, 2024
HiCEGNN
Public
A transformer method of reconstructing 3D structures of genomes and chromosomes from Hi-C data
Python
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MIT License
•0•2•0•0•Updated Sep 6, 2024Sep 6, 2024
tulip
Public
Template-based modeling for accurate prediction of ligand-protein complex structures (TULIP)
Python
•1•0•0•0•Updated Jun 5, 2024Jun 5, 2024
JCVIDB
Public
A data repository for JCVI minimum cells
JavaScript
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GNU General Public License v3.0
•0•0•0•0•Updated May 31, 2024May 31, 2024
SERSFormer
Public
Transformers for predicting food contamination
Python
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MIT License
•0•2•0•0•Updated Apr 16, 2024Apr 16, 2024
GCPNet-EMA
Public
Protein Structure Accuracy Estimation using Geometry-Complete Perceptron Networks (Protein Science 2024)
Python
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MIT License
•3•6•0•0•Updated Mar 25, 2024Mar 25, 2024
CDPred
Public
Deep transformer for predicting interchain residue-residue distances of protein complexes
Python
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MIT License
•3•12•1•0•Updated Mar 19, 2024Mar 19, 2024
DiffDock
Public
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
Python
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MIT License
•309•0•0•0•Updated Mar 4, 2024Mar 4, 2024
ScHiCEDRN
Public
Single cell 3D genome modeling tools developed in the Bioinformatics and Machine Learning Lab
Python
•1•5•1•0•Updated Jan 19, 2024Jan 19, 2024
CryoVirusDB
Public
A dataset of labeled virus particles in cryo-EM micrographs (images) for training and testing machine learning methods of virus particle picking
Python
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MIT License
•0•26•0•0•Updated Jan 9, 2024Jan 9, 2024
MULTICOM3
Public
The software system of improving AlphaFold2- and AlphaFold-Multimer-based protein tertiary & quaternary structure prediction. It was developed by the Bioinformatics and Machine Learning Lab at the University of Missouri. It was blindly tested in CASP15 and ranked among the best server predictors in 2022. It improves AlphaFold's accuracy by 5-10%.
Python
•8•28•0•0•Updated Dec 14, 2023Dec 14, 2023