proteins
There are 285 repositories under proteins topic.
aqlaboratory/proteinnet
Standardized data set for machine learning of protein structure
BradyAJohnston/MolecularNodes
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
microsoft/foldingdiff
Diffusion models of protein structure; trigonometry and attention are all you need!
HannesStark/EquiBind
EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
williamgilpin/pypdb
A Python API for the RCSB Protein Data Bank (PDB)
rdk/p2rank
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
octavian-ganea/equidock_public
EquiDock: geometric deep learning for fast rigid 3D protein-protein docking
Acellera/moleculekit
MoleculeKit: Your favorite molecule manipulation kit
biolib/openprotein
A PyTorch framework for prediction of tertiary protein structure
PDB-REDO/dssp
Application to assign secondary structure to proteins
soedinglab/plass
sensitive and precise assembly of short sequencing reads
bio4j/bio4j
Bio4j abstract model and general entry point to the project
Genentech/equifold
Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
lucidrains/progen
Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax
chao1224/Geom3D
Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023
samirelanduk/atomium
Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)
saezlab/OmnipathR
R client for the OmniPath web service
virtualramblas/awesome-deep-learning-4-life-sciences
A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).
haddocking/haddock3
Official repo of the modular BioExcel version of HADDOCK
BasedLabs/NoLabs
Open source biolab
diegozea/MIToS.jl
Mutual Information Tools for protein Sequence analysis in Julia
BioinfoMachineLearning/DeepInteract
A geometric deep learning pipeline for predicting protein interface contacts. (ICLR 2022)
anton-bushuiev/PPIRef
Dataset and package for working with protein-protein interactions in 3D
psipred/psipred
PSIPRED Protein Secondary Structure Predictor
sigven/oncoEnrichR
Cancer-dedicated gene set interpretation
Genentech/walk-jump
Official repository for discrete Walk-Jump Sampling (dWJS)
vsomnath/holoprot
Multi-Scale Representation Learning on Proteins (NeurIPS 2021)
mircare/Porter5
Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes
BioinfoMachineLearning/DIPS-Plus
The Enhanced Database of Interacting Protein Structures for Interface Prediction
aws-samples/amazon-sagemaker-protein-classification
Implementation of Protein Classification based on subcellular localization using ProtBert(Rostlab/prot_bert_bfd_localization) model from Hugging Face library, based on BERT model trained on large corpus of protein sequences.
OpenProteinAI/PoET
Inference code for PoET: A generative model of protein families as sequences-of-sequences
prescient-design/walk-jump
Official repository for discrete Walk-Jump Sampling (dWJS)
anton-bushuiev/PPIformer
Learning to design protein-protein interactions with enhanced generalization (ICLR24)
pmartR/pmartR
The pmartR R package provides functionality for quality control, normalization, exploratory data analysis, and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data.
mims-harvard/PINNACLE
Contextualizing protein representations using deep learning on protein networks and single-cell data
TurtleTools/geometricus
A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.