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@oxpig Oxford Protein Informatics Group

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    47 repositories

    • Graphinity

      Public
      Graphinity: Equivariant Graph Neural Network Architecture for Predicting Change in Antibody-Antigen Binding Affinity
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •6•25•0•0•Updated Dec 30, 2024Dec 30, 2024

    • AntiFold

      Public
      Improved antibody structure-based design using inverse folding
      antibodyantibody-design
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•82•1•0•Updated Dec 21, 2024Dec 21, 2024

    • Humatch

      Public
      Fast, gene-specific joint humanisation of antibody heavy and light chains.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•9•0•0•Updated Dec 11, 2024Dec 11, 2024

    • AEV-PLIG

      Public
      Python
      •
      Other
      •2•2•0•0•Updated Dec 2, 2024Dec 2, 2024

    • MolSnapper

      Public
      Python
      •
      MIT License
      •4•22•0•0•Updated Nov 9, 2024Nov 9, 2024

    • SPACE2

      Public
      Tool for rapid clustering of antibody models by the structure of their CDRs.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•19•0•0•Updated Nov 1, 2024Nov 1, 2024

    • ECFP-Sort-and-Slice

      Public
      Sort & Slice: A Simple and Superior Alternative to Hash-Based Folding for Extended-Connectivity Fingerprints (ECFPs)
      Jupyter Notebook
      •
      MIT License
      •4•5•0•0•Updated Oct 26, 2024Oct 26, 2024

    • CaLM

      Public
      Protein language model trained on coding DNA
      machine-learningdeep-learningcomputational-biologydnalanguage-modelscodonsprotein-language-modelllms
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•42•6•0•Updated Oct 20, 2024Oct 20, 2024

    • CoPriNet

      Public
      Deep learning for compound price prediction
      Python
      •
      MIT License
      •6•19•0•0•Updated Aug 22, 2024Aug 22, 2024

    • AbLang2

      Public
      An antibody-specific language model focusing on NGL prediction
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•23•0•0•Updated Aug 22, 2024Aug 22, 2024

    • p-IgGen

      Public
      p-IgGen: A Generative Paired Antibody Language Model
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•7•0•0•Updated Jul 10, 2024Jul 10, 2024

    • kasearch

      Public
      KA-Search: Rapid and exhaustive sequence identity search of known antibodies
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •9•21•0•0•Updated Jul 9, 2024Jul 9, 2024

    • PLAbDab

      Public
      The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •6•23•0•0•Updated Jul 8, 2024Jul 8, 2024

    • cesped

      Public
      Cryo-EM Supervised Pose Estimation Dataset utilities
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Jul 2, 2024Jul 2, 2024

    • ImmuneBuilder

      Public
      Predict the structure of immune receptor proteins
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •38•122•0•1•Updated Jun 25, 2024Jun 25, 2024

    • ANARCI

      Public
      Antibody Numbering and Antigen Receptor ClassIfication
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •93•193•45•11•Updated May 21, 2024May 21, 2024

    • sdAbs_vs_Abs

      Public
      A comparison of the binding sites of antibodies and single-domain antibodies
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated May 2, 2024May 2, 2024

    • Tz_her2_affinity_and_beyond

      Public
      Design and refine high affinity antibody libraries
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•0•Updated Mar 29, 2024Mar 29, 2024

    • binding-sites

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•6•0•0•Updated Mar 26, 2024Mar 26, 2024

    • DEVELOP

      Public
      Python
      •
      Other
      •17•56•0•0•Updated Mar 14, 2024Mar 14, 2024

    • Fragmenstein

      Public
      Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse
      Python
      •
      MIT License
      •13•3•0•0•Updated Feb 22, 2024Feb 22, 2024

    • molecular_rectifier

      Public
      Given an RDKit molecule that does not sanitise, correct it until it does
      Python
      •
      MIT License
      •7•0•0•0•Updated Feb 21, 2024Feb 21, 2024

    • DeepCoy

      Public
      Python
      •
      Other
      •17•30•0•0•Updated Feb 5, 2024Feb 5, 2024

    • OAS-CanonicalForms

      Public
      Code to perform clustering of antibody CDRs from predicted structures of sequences from the Observed Antibody Space.
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•0•Updated Jan 24, 2024Jan 24, 2024

    • Python_SmallWorld_API

      Public
      An (unofficial) Python3 module to query the SmallWorld chemical space search server (https://sw.docking.org/search.html)
      Python
      •
      MIT License
      •4•0•0•0•Updated Jan 17, 2024Jan 17, 2024

    • rdkit_to_params

      Public
      Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file
      Python
      •
      MIT License
      •5•0•0•0•Updated Dec 8, 2023Dec 8, 2023

    • AbLang

      Public
      AbLang: A language model for antibodies
      semanticprotein-sequenceslanguage-modelantibodies
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •24•132•2•1•Updated Sep 22, 2023Sep 22, 2023

    • SCALOP

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•8•2•1•Updated Sep 21, 2023Sep 21, 2023

    • Protein-Ligand-Interaction-Graphs

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •9•0•0•0•Updated Jun 10, 2023Jun 10, 2023

    • hummus

      Public template
      Code associated with generating figures from Richardson & Binter et al, 2022.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Apr 5, 2023Apr 5, 2023