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acdc-nn

beacon2-ri-api

Beacon v2 Reference Implementation (API)

beacon2-ri-tools

Beacon v2 Reference Implementation (Data ingestion tools)

bio-transformers

bio-transformers is a wrapper on top of the ESM/Protbert model, trained on millions on proteins and used to predict embeddings.

ddg-projects

ddgun

predict stability change upon mutation

ddgwizard

ddgwizard_tra_val

elaspic

Predicting the effect of mutations on protein stability and protein-protein interaction affinity.

elaspic-rest-api

Source code for the ELASPIC REST API: http://elaspic.kimlab.org/api/v1/docs.

elaspic-webserver

Source code for the ELASPIC web server: http://elaspic.kimlab.org.

elaspic2

Predicting the effect of mutations on protein stability and protein binding affinity using pretrained neural networks and a ranking objective function.

elaspic2-rest-api

Source code for the ELASPIC2 REST API: http://elaspic2-api.proteinsolver.org/docs.

fathmm

The Functional Analysis through Hidden Markov Models Software and Server

fathmm-mkl

Predict the functional consequences of both coding and non-coding single nucleotide variants (SNVs)

features_extraction

fellowship

ELIXIR-UK Fellowship – A Fellowship of UK ambassadors to build capacity in RDM for the life sciences

fellowship_website

galaxy

Data intensive science for everyone.

galaxy-beacon-import

import variants from galaxy datasets to a beacon instance

hydrocluster

The program Hydrocluster is designed to determine the position, size and content of hydrophobic, hydrophilic and charged clusters in protein molecules. The program is based on the DBSCAN algorithm.

kmbio

Fork of biopython for local development

kmtools

Bits of reusable code to make our lives easier. Follows the *whole sort of general mish-mash* design principle.

muscle

Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

prediction_and_validation

protein_folding_energy

Scripts for making a "protein folding energy" dataset.

proteinsolver

Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.

proteintools

The code as found in https://proteintools.uni-bayreuth.de/

protlego

Automated construction of protein chimeras and their analysis.

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.