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@labstructbioinf

Laboratory of Structural Bioinformatics

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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:

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  1. pLM-BLAST pLM-BLAST Public

    Detection of remote homology by comparison of protein language model representations

    Python 46 5

  2. localpdb localpdb Public

    Python package to manage protein structures and their annotations

    Python 41 5

  3. EdgeGat EdgeGat Public

    graph neural network layer for Deep Graph Library with pytorch backend

    Python 24 3

  4. DeepCoil DeepCoil Public

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

    Python 22 2

  5. rossmann-toolbox rossmann-toolbox Public

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

    Python 12 3

  6. PiPred PiPred Public

    Deep learning based prediction of pi-helices in protein sequences

    Python 10 1

Repositories

Showing 10 of 20 repositories
  • pLM-BLAST Public

    Detection of remote homology by comparison of protein language model representations

    labstructbioinf/pLM-BLAST’s past year of commit activity
    Python 46 MIT 5 6 0 Updated Dec 16, 2024
  • graph_toolbox Public

    utilities for processing protein structures

    labstructbioinf/graph_toolbox’s past year of commit activity
    Jupyter Notebook 4 0 0 0 Updated Sep 30, 2024
  • lbs-tools Public
    labstructbioinf/lbs-tools’s past year of commit activity
    Jupyter Notebook 7 1 1 1 Updated Jul 9, 2024
  • PLMAlign Public Forked from maovshao/PLMAlign

    PLMAlign utilizes per-residue embeddings as input to obtain specific alignments and more refined similarity

    labstructbioinf/PLMAlign’s past year of commit activity
    Jupyter Notebook 0 MIT 3 0 0 Updated Jun 5, 2024
  • PLMSearch Public template Forked from maovshao/PLMSearch

    PLMSearch enables accurate and fast homologous protein search with only sequences as input

    labstructbioinf/PLMSearch’s past year of commit activity
    Jupyter Notebook 0 MIT 8 0 0 Updated Jun 5, 2024
  • edi Public
    labstructbioinf/edi’s past year of commit activity
    HTML 2 0 0 0 Updated Apr 23, 2024
  • localpdb Public

    Python package to manage protein structures and their annotations

    labstructbioinf/localpdb’s past year of commit activity
    Python 41 MIT 5 3 0 Updated Feb 22, 2024
  • dc2_oligo Public

    Prediction of oligomeric state of coiled-coil domains

    labstructbioinf/dc2_oligo’s past year of commit activity
    Python 3 MIT 1 0 0 Updated Jan 18, 2024
  • HAMPpred Public

    Assessing the conformational landscape of the HAMP domain with AlphaFold2

    labstructbioinf/HAMPpred’s past year of commit activity
    Jupyter Notebook 3 0 0 1 Updated Dec 21, 2023
  • DeepCoil Public

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

    labstructbioinf/DeepCoil’s past year of commit activity
    Python 22 2 1 0 Updated Dec 17, 2023

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