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    55 repositories

    • mlschool

      Public
      Website for the Machine Learning Summerschool for Toxinologists
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • TMvisDB

      Public
      TMvisDB provides per-residue transmembrane topology annotations for all proteins in AlphaFold DB (~ 200 million proteins, September '22) predicted as transmembrane proteins (~ 46 million).
      Jupyter Notebook
      •
      Academic Free License v3.0
      •0•0•0•0•Updated Jul 18, 2024Jul 18, 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.
      savssingle-amino-acid-variantseffect-predictionmachine-learningbioinformaticsdeep-learning
      Python
      •
      GNU Affero General Public License v3.0
      •6•30•0•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

    • LambdaPP

      Public
      JavaScript
      •
      Academic Free License v3.0
      •0•4•0•0•Updated May 12, 2023May 12, 2023

    • goPredSim

      Public
      Python
      •
      MIT License
      •4•43•1•0•Updated May 8, 2023May 8, 2023

    • RostSpace

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •1•2•2•0•Updated Mar 15, 2023Mar 15, 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 functioning predictprotein suite, including all of its required methods. Databases are not included.
      Dockerfile
      •
      Other
      •7•13•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
      mlpubmedpubmed-centralpubmed-parserbionlprelationship-extractionpythonnlpner
      Python
      •
      Apache License 2.0
      •26•112•19•2•Updated Dec 8, 2022Dec 8, 2022

    • LocText

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

    • FunFamsClustering

      Public
      Python
      •1•9•1•0•Updated Oct 21, 2022Oct 21, 2022

    • EAT

      Public
      Embedding-based annotation transfer (EAT) uses Euclidean distance between vector representations (embeddings) of proteins to transfer annotations from a set of labeled lookup protein embeddings to query protein embedding.
      Python
      •
      GNU General Public License v3.0
      •7•28•1•0•Updated Oct 18, 2022Oct 18, 2022

    • LocTree3

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

    • bindPredict

      Public
      Prediction of binding residues for metal ions, nucleic acids, and small molecules.
      proteinspredictionembeddingsbinding-sitesbioinformatics
      Python
      •9•31•1•0•Updated Sep 15, 2022Sep 15, 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•1•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-learningpytorchprotein-predictiontransmembrane-proteinsprotein-embeddings
      0•0•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 TPUs using Transformers Models.
      Jupyter Notebook
      •
      Academic Free License v3.0
      •152•10•0•0•Updated Jun 2, 2022Jun 2, 2022

    • ConSurf

      Public
      Evolutionary conservation estimation of residues or nucleotides
      C++
      •
      GNU General Public License v3.0
      •12•32•11•0•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-predictionprotein-embeddings
      0•0•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

    • SeqVec

      Public
      Modelling the Language of Life - Deep Learning Protein Sequences
      bioinformaticsprotein-structureproteinprotein-function
      Python
      •
      MIT License
      •26•116•3•0•Updated Sep 15, 2020Sep 15, 2020

    • ProNA2020

      Public
      ProNA2020: System predicting protein-DNA, protein-RNA and protein-protein binding sites from sequence
      Python
      •2•14•1•0•Updated Aug 7, 2020Aug 7, 2020