Rostlab

nalaf

NLP framework in python for entity recognition and relationship extraction

SeqVec

Modelling the Language of Life - Deep Learning Protein Sequences

goPredSim

bindPredict

Prediction of binding residues for metal ions, nucleic acids, and small molecules.

ConSurf

Evolutionary conservation estimation of residues or nucleotides

VESPA

VESPA is a simple, yet powerful Single Amino Acid Variant (SAV) effect predictor based on embeddings of the Protein Language Model ProtT5.

EAT

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.

ProNA2020

ProNA2020: System predicting protein-DNA, protein-RNA and protein-protein binding sites from sequence

predictprotein-docker

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.

FunFamsClustering

nala

Text mining of natural language mutations mentions

ProtTrans

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.

LocText

Relation Extraction (RE) of: Proteins <--> Cell Compartments

LambdaPP

TMSEG

Transmembrane Proteins Predictor

LocNuclei

Prediction of subnuclear locations

PredictProtein

PredictProtein is an automatic service for protein database searches and the prediction of aspects of protein structure and function.

LocTree3

Protein Subcelullar Localization Sequenced-Based Predictor

ProNAhot

ProNAhot: Predicting protein-DNA, protein-RNA and protein-protein binding hot-spots from sequence

RostSpace

bindadjust

smiles-cl

TMvis

Combining AlphaFold 2 structures with predicted transmembrane proteins into interactive 3D visualizations of protein structures embedded into membranes.

bio_embeddings

Repository containing bio_embeddings resources

ppi_utils

TMbed

Transmembrane proteins predicted through Language Model embeddings

TMvisDB

TMvisDB provides per-residue transmembrane topology annotations for all proteins in AlphaFold DB (~ 200 million proteins, September '22) predicted as transmembrane proteins (~ 46 million).

blog

mlschool23

Website for the Machine Learning Summerschool for Toxinologists

SETH

Re-directing to the official SETH repository