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@labstructbioinf

Laboratory of Structural Bioinformatics

Welcome to our Github

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The amount of biological data available from different experimental approaches (genome and transcriptome sequencing, structure determination, functional assays) is enormous. In our group, we use computational techniques such as deep learning, molecular dynamics simulations and sequence analysis to make sense of this data. We are particularly interested in understanding how protein folds have evolved and how protein structures and functions are encoded by the 20 amino acid alphabet.

Useful links:

Pinned

  1. localpdb localpdb Public

    Python package to manage protein structures and their annotations

    Python 40 5

  2. pLM-BLAST pLM-BLAST Public

    Detection of remote homology by comparison of protein language model representations

    Python 36 3

  3. DeepCoil DeepCoil Public

    Fast and accurate prediction of coiled coil domains in protein sequences. ​

    Python 19 1

  4. EdgeGat EdgeGat Public

    graph neural network layer for Deep Graph Library with pytorch backend

    Python 17 3

  5. rossmann-toolbox rossmann-toolbox Public

    Prediction and re-engineering of the cofactor specificity of Rossmann-fold proteins

    Python 11 2

  6. PiPred PiPred Public

    Deep learning based prediction of pi-helices in protein sequences

    Python 10 1

Repositories

Showing 10 of 18 repositories
  • Jupyter Notebook 7 1 1 1 Updated Apr 26, 2024
  • pLM-BLAST Public

    Detection of remote homology by comparison of protein language model representations

    Python 36 MIT 3 4 0 Updated Apr 24, 2024
  • edi Public
    HTML 2 0 0 0 Updated Apr 23, 2024
  • graph_toolbox Public

    utilities for processing protein structures

    Jupyter Notebook 4 0 0 0 Updated Mar 27, 2024
  • localpdb Public

    Python package to manage protein structures and their annotations

    Python 40 MIT 5 0 0 Updated Feb 22, 2024
  • dc2_oligo Public

    Prediction of oligomeric state of coiled-coil domains

    Python 1 MIT 0 0 0 Updated Jan 18, 2024
  • HAMPpred Public

    Assessing the conformational landscape of the HAMP domain with AlphaFold2

    Jupyter Notebook 3 0 0 1 Updated Dec 21, 2023
  • DeepCoil Public

    Fast and accurate prediction of coiled coil domains in protein sequences. ​

    Python 19 1 0 0 Updated Dec 17, 2023
  • rossmann-toolbox Public

    Prediction and re-engineering of the cofactor specificity of Rossmann-fold proteins

    Python 11 MIT 2 1 0 Updated Nov 5, 2023
  • PiPred Public

    Deep learning based prediction of pi-helices in protein sequences

    Python 10 1 0 5 Updated Mar 24, 2023

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