Repositories list

• TMvisDB

  Public archive
  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 Nov 13, 2024Nov 13, 2024

• mlschool

  Public
  Website for the Machine Learning Summerschool for Toxinologists

  JavaScript

  •

  MIT License

  •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• RostSpace

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •1•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.

  savssingle-amino-acid-variantseffect-prediction+ 3machine-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

• 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-central+ 6pubmed-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

  nlpnluml+ 3textminingproteincell-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.

  proteinspredictionembeddings+ 2binding-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-learning+ 4pytorchprotein-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

  •153•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•33•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-prediction+ 1protein-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-structureprotein+ 1protein-function

  Python

  •

  MIT License

  •26•118•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