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    47 repositories

    • deep-learning-hpc-project-template

      Public
      A PyTorch Lightning project template adapted for high-performance computing clusters such as Summit and Fugaku
      Python
      •
      Apache License 2.0
      •2•6•0•2•Updated Apr 13, 2026Apr 13, 2026

    • PoseBench

      Public
      Comprehensive benchmarking of protein-ligand structure prediction methods. (Nature Machine Intelligence)
      benchmarkmachine-learningdeep-learning
      benchmarkmachine-learningdeep-learningcomputational-biologycomputational-chemistrystructure-predictionmolecular-docking
      Jupyter Notebook
      •
      MIT License
      •17•220•1•0•Updated Mar 24, 2026Mar 24, 2026

    • GRNformer

      Public
      Transformer models for predicting gene regulatory networks from omics data
      Python
      •
      MIT License
      •3•19•0•0•Updated Mar 4, 2026Mar 4, 2026

    • CAF3

      Public
      Engineering Multiple Sequence Alignments and Templates to Improve AlphaFold3 for Protein and Ligand Structure Prediction
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 4, 2026Mar 4, 2026

    • PSBench

      Public
      A large and comprehensive benchmark for estimating the accuracy of protein complex structural models
      C
      •
      MIT License
      •1•10•0•0•Updated Feb 4, 2026Feb 4, 2026

    • TFBindFormer

      Public
      A cross-attention transformer for predicting transcription factor-DNA binding
      Python
      •
      MIT License
      •0•2•0•0•Updated Feb 2, 2026Feb 2, 2026

    • 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
      •
      MIT License
      •0•26•0•0•Updated Jan 27, 2026Jan 27, 2026

    • TransFew

      Public
      Transformer for protein function prediction (version 2)
      Jupyter Notebook
      •
      MIT License
      •0•14•1•0•Updated Jan 8, 2026Jan 8, 2026

    • MULTICOM_ligand

      Public
      Comprehensive ensembling of protein-ligand structure and affinity prediction methods (CASP16)
      deep-learningdrug-discoveryprotein-ligand-interactions
      deep-learningdrug-discoveryprotein-ligand-interactionsdiffusion-modelbinding-affinitypose-predictionflow-matching
      Jupyter Notebook
      •
      MIT License
      •0•8•0•1•Updated Jan 6, 2026Jan 6, 2026

    • gate

      Public
      Graph transformer for estimating protein model accuracy
      C
      •1•5•1•0•Updated Jan 3, 2026Jan 3, 2026

    • MULTICOM4

      Public
      The MULTICOM4 protein structure prediction system developed by the Bioinformatics and Machine Learning Lab at the University of Missouri - Columbia
      Python
      •
      Other
      •6•17•0•0•Updated Nov 27, 2025Nov 27, 2025

    • FlowDock

      Public
      A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)
      machine-learningdeep-learningcomputational-biology
      machine-learningdeep-learningcomputational-biologycomputational-chemistrygenerative-modelstructure-predictionmolecular-docking
      Python
      •
      MIT License
      •26•132•1•0•Updated Sep 3, 2025Sep 3, 2025

    • DIPS-Plus

      Public
      The Enhanced Database of Interacting Protein Structures for Interface Prediction
      machine-learningbioinformaticsdeep-learning
      machine-learningbioinformaticsdeep-learningproteinsdatasets
      Python
      •
      GNU General Public License v3.0
      •9•55•5•0•Updated Aug 29, 2025Aug 29, 2025

    • denoisecryodata

      Public
      The dataset for training machine learning methods to denoise cryo-EM density maps
      Python
      •
      MIT License
      •0•3•1•0•Updated Jul 5, 2025Jul 5, 2025

    • .github

      Public
      0•0•0•0•Updated Jun 12, 2025Jun 12, 2025

    • mintomics

      Public
      Python
      •
      MIT License
      •3•2•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-learningdeep-learningcomputational-biology
      machine-learningdeep-learningcomputational-biologycomputational-chemistrygenerative-modelgraph-neural-networks
      Python
      •
      Other
      •33•235•0•0•Updated May 30, 2025May 30, 2025

    • GCPNet

      Public
      A geometry-complete SE(3)-equivariant perceptron network (GCPNet) for 3D graphs. (Bioinformatics)
      machine-learningdeep-learningcomputational-biology
      machine-learningdeep-learningcomputational-biologygraph-neural-networks
      Python
      •
      MIT License
      •5•53•0•0•Updated Apr 20, 2025Apr 20, 2025

    • chai-lab

      Public
      Chai-1, SOTA model for biomolecular structure prediction
      Python
      •
      Apache License 2.0
      •265•1•0•0•Updated Apr 15, 2025Apr 15, 2025

    • openfold-triton-evoformer

      Public
      Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
      Python
      •
      Apache License 2.0
      •668•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
      •
      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
      •
      MIT License
      •1•4•2•0•Updated Jan 21, 2025Jan 21, 2025

    • GCDM-SBDD

      Public
      A geometry-complete diffusion generative model (GCDM) for structure-based drug design (Nature CommsChem)
      Python
      •
      MIT License
      •5•24•0•0•Updated Nov 6, 2024Nov 6, 2024

    • cryo2struct

      Public
      The programs for preprocessing cryo-EM density maps for machine learning
      Python
      •
      MIT License
      •2•32•1•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
      •
      MIT License
      •1•4•1•0•Updated Sep 6, 2024Sep 6, 2024

    • tulip

      Public
      Template-based modeling for accurate prediction of ligand-protein complex structures (TULIP)
      Python
      •1•1•0•0•Updated Jun 5, 2024Jun 5, 2024

    • JCVIDB

      Public
      A data repository for JCVI minimum cells
      JavaScript
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 31, 2024May 31, 2024

    • SERSFormer

      Public
      Transformers for predicting food contamination
      Python
      •
      MIT License
      •1•4•0•0•Updated Apr 16, 2024Apr 16, 2024

    • GCPNet-EMA

      Public
      Protein Structure Accuracy Estimation using Geometry-Complete Perceptron Networks (Protein Science 2024)
      Python
      •
      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
      •
      MIT License
      •3•14•1•0•Updated Mar 19, 2024Mar 19, 2024
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