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    57 repositories

    • pbc

      Public
      Protein (language model) Benchmarking Collection - PBC
      protein-structureproteinprotein-disorder
      protein-structureproteinprotein-disorderprotein-localizationprotein-language-models
      Python
      •
      Academic Free License v3.0
      •0•3•0•0•Updated Apr 23, 2026Apr 23, 2026

    • pp-status

      Public
      Status Page for Predict Protein
      HTML
      •0•0•0•0•Updated Feb 24, 2026Feb 24, 2026

    • mlschool

      Public
      Website for the Machine Learning Summerschool for Toxinologists
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Dec 17, 2025Dec 17, 2025

    • bindPredict

      Public
      Prediction of binding residues for metal ions, nucleic acids, and small molecules.
      bioinformaticsproteinsprediction
      bioinformaticsproteinspredictionembeddingsbinding-sites
      Python
      •
      MIT License
      •10•37•2•0•Updated Sep 2, 2025Sep 2, 2025

    • EAT

      Public
      Embedding-based annotation transfer (EAT) uses Euclidean distance between vector representations (embeddings) of proteins to transfer annotations from a set of …
      Python
      •
      GNU General Public License v3.0
      •7•41•1•0•Updated Aug 29, 2025Aug 29, 2025

    • LambdaPP

      Public
      JavaScript
      •
      Academic Free License v3.0
      •1•4•0•0•Updated May 12, 2025May 12, 2025

    • goPredSim

      Public
      Python
      •
      MIT License
      •4•51•0•0•Updated Dec 2, 2024Dec 2, 2024

    • TMvisDB

      Public archive
      TMvisDB provides per-residue transmembrane topology annotations for all proteins in AlphaFold DB (~ 200 million proteins, September '22) predicted as transmembr…
      Jupyter Notebook
      •
      Academic Free License v3.0
      •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

    • RostSpace

      Public archive
      Python
      •
      GNU Affero General Public License v3.0
      •0•2•2•0•Updated Oct 17, 2024Oct 17, 2024

    • VESPA

      Public
      VESPA is a simple, yet powerful Single Amino Acid Variant (SAV) effect predictor based on embeddings of the Protein Language Model ProtT5.
      machine-learningbioinformaticsdeep-learning
      machine-learningbioinformaticsdeep-learningsavssingle-amino-acid-variantseffect-prediction
      Python
      •
      GNU Affero General Public License v3.0
      •9•35•1•0•Updated Mar 4, 2024Mar 4, 2024

    • smiles-cl

      Public
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Aug 15, 2023Aug 15, 2023

    • blog

      Public
      TypeScript
      •
      MIT License
      •0•0•0•0•Updated Aug 3, 2023Aug 3, 2023

    • ppi_utils

      Public
      Python
      •
      Academic Free License v3.0
      •0•0•0•0•Updated Mar 14, 2023Mar 14, 2023

    • predictprotein-docker

      Public
      Based off of the official Rostlab & PredictProtein website installation, as of 2020-09-07, the produced Docker image from this repository will result in a fully…
      Dockerfile
      •
      Other
      •7•14•2•0•Updated Feb 13, 2023Feb 13, 2023

    • nala

      Public
      Text mining of natural language mutations mentions
      HTML
      •5•6•16•2•Updated Dec 8, 2022Dec 8, 2022

    • nalaf

      Public
      NLP framework in python for entity recognition and relationship extraction
      pythonnlpml
      pythonnlpmlpubmedpubmed-centralpubmed-parsernerbionlprelationship-extraction
      Python
      •
      Apache License 2.0
      •24•115•19•2•Updated Dec 8, 2022Dec 8, 2022

    • LocText

      Public
      Relation Extraction (RE) of: Proteins <--> Cell Compartments
      nlpnluml
      nlpnlumlproteintextminingcell-compartments
      HTML
      •
      Apache License 2.0
      •2•5•6•6•Updated Dec 8, 2022Dec 8, 2022

    • FunFamsClustering

      Public
      Python
      •1•11•1•0•Updated Oct 21, 2022Oct 21, 2022

    • LocTree3

      Public
      Protein Subcelullar Localization Sequenced-Based Predictor
      Roff
      •
      Other
      •1•2•3•0•Updated Sep 29, 2022Sep 29, 2022

    • TMvis

      Public
      Combining AlphaFold 2 structures with predicted transmembrane proteins into interactive 3D visualizations of protein structures embedded into membranes.
      Python
      •
      MIT License
      •0•2•0•0•Updated Sep 2, 2022Sep 2, 2022

    • bindadjust

      Public
      Python
      •0•1•0•0•Updated Aug 31, 2022Aug 31, 2022

    • SETH

      Public
      Re-directing to the official SETH repository
      0•0•0•0•Updated Jun 21, 2022Jun 21, 2022

    • TMbed

      Public
      Transmembrane proteins predicted through Language Model embeddings
      machine-learningbioinformaticsdeep-learning
      machine-learningbioinformaticsdeep-learningpytorchprotein-predictiontransmembrane-proteinsprotein-embeddings
      0•1•0•0•Updated Jun 12, 2022Jun 12, 2022

    • ProtTrans

      Public
      ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google T…
      Jupyter Notebook
      •
      Academic Free License v3.0
      •167•11•0•0•Updated Jun 2, 2022Jun 2, 2022

    • ConSurf

      Public
      Evolutionary conservation estimation of residues or nucleotides
      C++
      •
      GNU General Public License v3.0
      •25•64•15•1•Updated Mar 28, 2022Mar 28, 2022

    • TMSEG

      Public
      Transmembrane Proteins Predictor
      Roff
      •
      GNU General Public License v3.0
      •2•4•1•0•Updated Feb 4, 2022Feb 4, 2022

    • LocNuclei

      Public
      Prediction of subnuclear locations
      Python
      •1•3•1•0•Updated Jul 8, 2021Jul 8, 2021

    • PredictProtein

      Public
      PredictProtein is an automatic service for protein database searches and the prediction of aspects of protein structure and function.
      Perl
      •
      Academic Free License v3.0
      •1•3•0•0•Updated May 20, 2021May 20, 2021

    • bio_embeddings

      Public
      Repository containing bio_embeddings resources
      bioinformaticsprotein-structureprotein-prediction
      bioinformaticsprotein-structureprotein-predictionprotein-embeddings
      0•1•0•0•Updated Jan 2, 2021Jan 2, 2021

    • ProNAhot

      Public
      ProNAhot: Predicting protein-DNA, protein-RNA and protein-protein binding hot-spots from sequence
      Python
      •
      MIT License
      •2•2•0•0•Updated Nov 17, 2020Nov 17, 2020
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