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    41 repositories

    • denoisecryodata

      Public
      The dataset for training machine learning methods to denoise cryo-EM density maps
      MIT License
      •0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

    • gate

      Public
      Graph transformer for estimating protein model accuracy
      C
      •0•1•0•0•Updated Feb 10, 2025Feb 10, 2025

    • MULTICOM_ligand

      Public
      Comprehensive ensembling of protein-ligand structure and affinity prediction methods (CASP16)
      deep-learningdrug-discoveryprotein-ligand-interactionsdiffusion-modelbinding-affinitypose-predictionflow-matching
      Jupyter Notebook
      •
      MIT License
      •0•7•0•0•Updated Feb 10, 2025Feb 10, 2025

    • PoseBench

      Public
      Comprehensive benchmarking of protein-ligand structure prediction methods (ICML 2024 AI4Science)
      Jupyter Notebook
      •
      MIT License
      •3•123•1•0•Updated Feb 10, 2025Feb 10, 2025

    • Cryo2Strut2

      Public
      The second version of Cryo2Struct for reconstructing protein structures from cryo-EM density maps
      MIT License
      •0•0•0•0•Updated Feb 9, 2025Feb 9, 2025

    • GRNformer

      Public
      Transformer models for predicting gene regulatory networks from omics data
      Python
      •
      MIT License
      •0•3•0•0•Updated Jan 29, 2025Jan 29, 2025

    • FlowDock

      Public
      Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction (CASP16)
      Python
      •
      MIT License
      •8•72•0•0•Updated Jan 24, 2025Jan 24, 2025

    • hicdiff

      Public
      Diffusion models for denoising Hi-C chromosome conformation capturing data
      Python
      •
      MIT License
      •0•3•2•0•Updated Jan 21, 2025Jan 21, 2025

    • TransFew

      Public
      Transformer for protein function prediction (version 2)
      Jupyter Notebook
      •
      MIT License
      •0•11•1•0•Updated Dec 20, 2024Dec 20, 2024

    • MULTICOM4

      Public
      The MULTICOM4 protein structure prediction system developed by the Bioinformatics and Machine Learning Lab at the University of Missouri - Columbia
      Python
      •1•4•0•0•Updated Dec 18, 2024Dec 18, 2024

    • GCDM-SBDD

      Public
      A geometry-complete diffusion generative model (GCDM) for structure-based drug design (Nature CommsChem)
      Python
      •
      MIT License
      •3•11•0•0•Updated Nov 6, 2024Nov 6, 2024

    • cryo2struct

      Public
      The programs for preprocessing cryo-EM density maps for machine learning
      Python
      •
      MIT License
      •1•24•0•0•Updated Oct 1, 2024Oct 1, 2024

    • bio-diffusion

      Public
      A geometry-complete diffusion generative model (GCDM) for 3D molecule generation and optimization (Nature CommsChem)
      Python
      •
      Other
      •26•188•1•0•Updated Sep 7, 2024Sep 7, 2024

    • HiCEGNN

      Public
      A transformer method of reconstructing 3D structures of genomes and chromosomes from Hi-C data
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • mintomics

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Jul 2, 2024Jul 2, 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
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 31, 2024May 31, 2024

    • GCPNet

      Public
      A PyTorch implementation of Geometry-Complete SE(3)-Equivariant Perceptron Networks (GCPNets)
      Python
      •
      MIT License
      •5•42•0•0•Updated May 5, 2024May 5, 2024

    • SERSFormer

      Public
      Transformers for predicting food contamination
      Python
      •
      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
      •
      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•12•1•0•Updated Mar 19, 2024Mar 19, 2024

    • DiffDock

      Public
      Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
      Python
      •
      MIT License
      •283•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•3•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
      •
      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

    • openfold-bugfixes

      Public
      Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
      Python
      •
      Apache License 2.0
      •568•0•0•0•Updated Dec 8, 2023Dec 8, 2023

    • FunBench

      Public
      The programs and data for benchmarking protein function site prediction methods
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Oct 7, 2023Oct 7, 2023

    • DProQ

      Public
      Deep learning prediction of protein complex structure quality
      Python
      •
      MIT License
      •4•6•2•1•Updated Sep 20, 2023Sep 20, 2023

    • cryoppp

      Public
      The programs of creating cryo-EM particle picking datasets
      Python
      •
      MIT License
      •5•69•0•0•Updated Sep 14, 2023Sep 14, 2023

    • DIPS-Plus

      Public
      The Enhanced Database of Interacting Protein Structures for Interface Prediction
      machine-learningbioinformaticsdeep-learningproteinsdatasets
      Python
      •
      GNU General Public License v3.0
      •8•48•5•0•Updated Sep 11, 2023Sep 11, 2023