m-westberg

m-westberg's Stars

• plinder-org/plinder

  Protein Ligand INteraction Dataset and Evaluation Resource

  Language:Python893

• pinder-org/pinder

  PINDER: The Protein INteraction Dataset and Evaluation Resource

  Language:Python521

• westlake-repl/SaprotHub

  SaprotHub: Making Protein Modeling Accessible to All Biologists

  Language:Jupyter Notebook375

• ProteinDesignLab/protpardelle

  Diffusion-based all-atom protein generative model.

  Language:Python13111

• Jonas-Verhellen/Bayesian-Illumination

  Bayesian Illumination is an accelerated generative model for optimization of small molecules.

  Language:Python12

• luwei0917/DynamicBind

  repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

  Language:Jupyter Notebook16435

• BioinfoMachineLearning/PoseBench

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

  Language:Jupyter Notebook491

• kyegomez/AlphaFold3

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

  Language:Python63783

• lucidrains/alphafold3-pytorch

  Implementation of Alphafold 3 in Pytorch

  Language:Python72759

• kreshuklab/go-nuclear

  Guides and code for 3D nuclear instance segmentation

  Language:Python193

• computational-cell-analytics/micro-sam

  Segment Anything for Microscopy

  Language:Jupyter Notebook31437

• baker-laboratory/RoseTTAFold-All-Atom

  Language:Python582100

• patrickbryant1/EvoBind

  In silico directed evolution of peptide binders with AlphaFold

  Language:Jupyter Notebook7515

• KULL-Centre/FRETpredict

  Software for the prediction of FRET data from conformational ensembles.

  Language:Jupyter Notebook223

• lehner-lab/MoCHI

  Neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis and allostery from deep mutational scanning data

  Language:Python282

• aelefebv/nellie

  Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy

  Language:Python283

• evo-design/evo

  Biological foundation modeling from molecular to genome scale

  Language:Jupyter Notebook895102

• bene837/af2seq

  Language:Python306

• andrew-cr/discrete_flow_models

  Code for the paper https://arxiv.org/abs/2402.04997

  Language:Python361

• bjing2016/alphaflow

  AlphaFold Meets Flow Matching for Generating Protein Ensembles

  Language:Python30543

• zrqiao/NeuralPLexer

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

  Language:Jupyter Notebook23864

• dauparas/LigandMPNN

  Language:Python18737

• instadeepai/FrameDiPT

  FrameDiPT: an SE(3) diffusion model for protein structure inpainting

  Language:Jupyter Notebook474

• microsoft/protein-frame-flow

  Fast protein backbone generation with SE(3) flow matching.

  Language:Python16010

• rdkibler/superfold

  Language:Python63

• Kuhlman-Lab/ThermoMPNN

  GNN trained to predict changes in thermodynamic stability for protein point mutants

  Language:Python9316

• bioimage-io/bioimageio-chatbot

  Your Personal Assistant in Computational Bioimaging.

  Language:Jupyter Notebook1710

• Kuhlman-Lab/evopro

  Language:Python566

• generatebio/chroma

  A generative model for programmable protein design

  Language:Python63978

• patrickbryant1/Umol

  Protein-ligand structure prediction

  Language:Jupyter Notebook17016