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    27 repositories

    • NaturalPPLuM

      Public
      Repository of the paper "Exploring sequence landscape of biosynthetic gene clusters with protein language models" published at ICML2024 workshop Machine Learning for Life and Material Science: From Theory to Industry applications
      deep-learningtransfer-learningbiosynthetic-gene-clusterssmall-dataicml-2024esm2ml4lms
      Jupyter Notebook
      •0•3•0•0•Updated Mar 7, 2025Mar 7, 2025

    • SMTB2024

      Public
      Python
      •1•1•1•2•Updated Mar 3, 2025Mar 3, 2025

    • DataSAIL

      Public
      DataSAIL is a tool to split datasets while reducing information leakage.
      machine-learningoptimizationilpscipdataset-splitilp-problem
      Python
      •
      MIT License
      •1•20•6•0•Updated Mar 3, 2025Mar 3, 2025

    • GlyLES

      Public
      A tool to convert IUPAC representations of glycans into SMILES strings.
      antlr4smilesgrammar-parserglycansiupac
      Python
      •
      MIT License
      •6•12•1•0•Updated Feb 22, 2025Feb 22, 2025

    • StructMAn

      Public
      Python
      •
      GNU Lesser General Public License v2.1
      •0•1•0•0•Updated Feb 17, 2025Feb 17, 2025

    • ALPAR

      Public
      Single Reference Antimicrobial Resistance
      machine-learningamrsingle-reference-amr
      Python
      •
      MIT License
      •0•1•5•0•Updated Jan 31, 2025Jan 31, 2025

    • EpiPAMPAS

      Public
      Rapid detection of intra-protein epistasis via parsimonious ancestral state reconstruction and counting parallel mutations
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • ProtPreTrain

      Public
      Protein structure pretraining
      Python
      •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • LP-PDBBind

      Public
      Jupyter Notebook
      •3•0•0•0•Updated Feb 1, 2024Feb 1, 2024

    • GraphPLI

      Public
      Structure-informed Prediction of Interactions of Lectins and Glycans
      Python
      •0•0•0•0•Updated Nov 27, 2023Nov 27, 2023

    • alphafold_non_docker

      Public
      AlphaFold2 non-docker setup
      Shell
      •121•352•21•2•Updated Nov 24, 2023Nov 24, 2023

    • useful_scripts

      Public
      A repository to share our useful scripts in, between our group and others
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Sep 19, 2023Sep 19, 2023

    • SMTB_2023

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 23, 2023Aug 23, 2023

    • CompressBinaryTable

      Public
      Compresses binary tables
      Python
      •0•0•0•0•Updated Jun 2, 2023Jun 2, 2023

    • datasail_tape

      Public
      Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •130•0•0•0•Updated Mar 24, 2023Mar 24, 2023

    • scala

      Public
      Python
      •0•0•0•0•Updated Feb 6, 2023Feb 6, 2023

    • panpa

      Public
      PanPA is a tool for generating alignment of protein graphs
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 21, 2022Nov 21, 2022

    • data-versioning-examples

      Public
      Examples of data stored under version control systems & list of various resources for data stewardship
      MIT License
      •0•1•0•0•Updated Oct 11, 2022Oct 11, 2022

    • SMTB2022

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Aug 5, 2022Aug 5, 2022

    • openfold_non_docker

      Public
      OpenFold non-docker setup
      alphafold2openfoldnon-docker
      Shell
      •1•3•0•0•Updated Aug 4, 2022Aug 4, 2022

    • d-StructMAn

      Public
      Python
      •
      GNU Lesser General Public License v2.1
      •0•2•1•0•Updated Jul 5, 2022Jul 5, 2022

    • metaprofi

      Public
      MetaProFi is a bloom filter based tool for storing and querying sequence data for accurate identification of functionally relevant genetic variants
      Python
      •
      GNU General Public License v2.0
      •2•12•1•0•Updated Apr 14, 2022Apr 14, 2022

    • rindti

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Mar 23, 2022Mar 23, 2022

    • rinminer

      Public
      RINminer is a frequent subgraph mining tool based on the gSpan algorithm with additional features and optimizations for residue interaction networks (RINs).
      C
      •
      MIT License
      •0•8•0•0•Updated May 2, 2021May 2, 2021

    • GraphDTA_PDBbind

      Public
      GraphDTA: Predicting drug-target binding affinity with graph neural networks on the PDBbind dataset
      Python
      •81•0•0•0•Updated Apr 13, 2021Apr 13, 2021

    • QCQP

      Public
      A CVXPY extension for handling nonconvex QCQP via Suggest-and-Improve framework
      Python
      •
      MIT License
      •26•0•0•0•Updated May 4, 2020May 4, 2020

    • spherecon

      Public
      This tool calculates a measure for relative solvent accessible area for single residues or whole amino acid chains.
      Python
      •
      GNU Lesser General Public License v3.0
      •0•3•0•0•Updated Mar 17, 2020Mar 17, 2020