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    20 repositories

    • pLM-BLAST

      Public
      Detection of remote homology by comparison of protein language model representations
      bioinformaticsprotein-language-modelprotein-sequence-embeddingscomputional-biology
      Python
      •
      MIT License
      •5•46•6•0•Updated Dec 16, 2024Dec 16, 2024

    • graph_toolbox

      Public
      utilities for processing protein structures
      pdb
      Jupyter Notebook
      •0•4•0•0•Updated Sep 30, 2024Sep 30, 2024

    • lbs-tools

      Public
      Jupyter Notebook
      •1•7•1•1•Updated Jul 9, 2024Jul 9, 2024

    • PLMAlign

      Public
      PLMAlign utilizes per-residue embeddings as input to obtain specific alignments and more refined similarity
      Jupyter Notebook
      •
      MIT License
      •3•0•0•0•Updated Jun 5, 2024Jun 5, 2024

    • PLMSearch

      Public template
      PLMSearch enables accurate and fast homologous protein search with only sequences as input
      Jupyter Notebook
      •
      MIT License
      •8•0•0•0•Updated Jun 5, 2024Jun 5, 2024

    • edi

      Public
      HTML
      •0•2•0•0•Updated Apr 23, 2024Apr 23, 2024

    • localpdb

      Public
      Python package to manage protein structures and their annotations
      bioinformatics-databasesstructural-bioinformaticsbioinformatics-tool
      Python
      •
      MIT License
      •5•41•3•0•Updated Feb 22, 2024Feb 22, 2024

    • dc2_oligo

      Public
      Prediction of oligomeric state of coiled-coil domains
      Python
      •
      MIT License
      •1•3•0•0•Updated Jan 18, 2024Jan 18, 2024

    • HAMPpred

      Public
      Assessing the conformational landscape of the HAMP domain with AlphaFold2
      Jupyter Notebook
      •0•3•0•1•Updated Dec 21, 2023Dec 21, 2023

    • DeepCoil

      Public
      Fast and accurate prediction of coiled coil domains in protein sequences. ​
      machine-learningbioinformaticscoiled-coilbioinformatics-toolprotein-sequences
      Python
      •2•22•1•0•Updated Dec 17, 2023Dec 17, 2023

    • rossmann-toolbox

      Public
      Prediction and re-engineering of the cofactor specificity of Rossmann-fold proteins
      bioinformatics
      Python
      •
      MIT License
      •3•12•1•0•Updated Nov 5, 2023Nov 5, 2023

    • PiPred

      Public
      Deep learning based prediction of pi-helices in protein sequences
      Python
      •1•10•0•5•Updated Mar 24, 2023Mar 24, 2023

    • .github

      Public
      0•0•0•0•Updated Mar 14, 2023Mar 14, 2023

    • ColabFold

      Public
      Making Protein folding accessible to all!
      Jupyter Notebook
      •
      MIT License
      •507•0•0•0•Updated Mar 7, 2023Mar 7, 2023

    • Uni-Fold

      Public
      An open-source platform for developing protein models beyond AlphaFold.
      Python
      •
      Apache License 2.0
      •74•0•0•0•Updated Nov 25, 2022Nov 25, 2022

    • samcc_turbo

      Public
      Software for automatic detection and measurement of coiled coils in PDB structures.
      Python
      •
      MIT License
      •2•3•0•0•Updated Sep 2, 2022Sep 2, 2022

    • EdgeGat

      Public
      graph neural network layer for Deep Graph Library with pytorch backend
      Python
      •3•24•0•0•Updated Oct 18, 2021Oct 18, 2021

    • localpdb-mybinder

      Public
      localpdb mybinder example
      Jupyter Notebook
      •0•0•0•0•Updated Jun 14, 2021Jun 14, 2021

    • DeepCoil_Paper_2018

      Public
      Scripts and jupyter notebooks necessary to replicate the analyses presented in the DeepCoil paper 2018.
      Jupyter Notebook
      •0•3•0•0•Updated Sep 21, 2018Sep 21, 2018

    • MDDesign

      Public
      Set of scripts that facilitate molecular dynamics aided screening of the models generated with Rosetta and selection of the structural ensembles that can be used as input in protein design simulations.
      Python
      •2•2•0•0•Updated Jul 4, 2017Jul 4, 2017