proteins

There are 6 repositories under proteins topic.

aqlaboratory / proteinnet
Standardized data set for machine learning of protein structure
machine-learning deep-learning protein-structure dataset protein-sequence proteins
Language:Python 850
MolecularNodes
BradyAJohnston / MolecularNodes
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
blender biochemistry geometry-nodes protein protein-structure protein-visualization sciart visualisation structural-biology blender-addon protein-data-bank molecule proteins pdb molecular-modeling
Language:Python 833
microsoft / foldingdiff
Diffusion models of protein structure; trigonometry and attention are all you need!
diffusion diffusion-models protein protein-structure-generation proteins transformer
Language:Jupyter Notebook 487
HannesStark / EquiBind
EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
geometry graph-neural-networks proteins protein-structure drug-discovery molecules equivariance
Language:Python 464
williamgilpin / pypdb
A Python API for the RCSB Protein Data Bank (PDB)
pdb blast proteomics protein-structure protein-sequences proteins protein-data-bank
Language:Python 301
p2rank
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.
bioinformatics machine-learning protein-structure pdb binding-sites proteins ligand protein-surface structural-bioinformatics protein-ligand-interactions java random-forest mmcif pymol groovy protein-ligand-docking molecular-structures drug-discovery virtual-screening p2rank
Language:Groovy 231
octavian-ganea / equidock_public
EquiDock: geometric deep learning for fast rigid 3D protein-protein docking
geometry proteins protein-protein-interaction docking graphneuralnetwork deeplearning equivariant-network equivariance equivariant-representations drugdiscovery drug-discovery
Language:Roff 226
Acellera / moleculekit
MoleculeKit: Your favorite molecule manipulation kit
molecule machine-learning proteins drug-discovery molecular-modeling molecular-simulation
Language:Python 193
biolib / openprotein
A PyTorch framework for prediction of tertiary protein structure
protein-structure proteins
Language:Python 178
PDB-REDO / dssp
Application to assign secondary structure to proteins
dssp pdb proteins
Language:C++ 146
plass
soedinglab / plass
sensitive and precise assembly of short sequencing reads
bioinformatics metagenomics sequence-assembler proteins opensource proteomics metatranscriptomics
Language:C 131
bio4j / bio4j
Bio4j abstract model and general entry point to the project
bio4j graph bioinformatics database graph-schema bio4j-titan property-graph titan protein proteins uniprot gene-ontology ncbi-taxonomy uniref graph-database graph-data graph-databases java java-8 graph-queries
Language:Java 118
Genentech / equifold
Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
machine-learning structure-prediction proteins structural-biology
Language:Python 116
lucidrains / progen
Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax
artificial-intelligence deep-learning proteins
Language:Python 109
chao1224 / Geom3D
Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023
3d 3d-structures biology chemistry crystals drugs equivariance geometry group invariance molecules physics proteins symmetry material ai4science
Language:Python 105
samirelanduk / atomium
Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)
biology proteins structural-biology chemistry molecules
Language:Python 102
saezlab / OmnipathR
R client for the OmniPath web service
omnipath complexes proteins enzyme-ptm pathways networks networks-biology
Language:R 94
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).
biotech cheminformatics deeplearning drug-discovery drug-repurposing molecules pharmaceuticals proteins python
94
haddock3
haddocking / haddock3
Official repo of the modular BioExcel version of HADDOCK
utrecht-university python3 workflows modelling docking proteins complexes integrative-modeling bioinformatics
Language:Python 84
BasedLabs / NoLabs
Open source biolab
ai bioinformatics folding webserver biolab proteins synthetic-biology
Language:Python 76
diegozea / MIToS.jl
Mutual Information Tools for protein Sequence analysis in Julia
bioinformatics protein-sequence-analysis protein-structure protein-evolution coevolution mutual-information conservation structural-bioinformatics pfam pdb sifts multiple-sequence-alignment julia-language biology proteins
Language:Julia 65
DeepInteract
BioinfoMachineLearning / DeepInteract
A geometric deep learning pipeline for predicting protein interface contacts. (ICLR 2022)
bioinformatics proteins transformers geometric-deep-learning graph-neural-networks protein-protein-interactions deep-learning machine-learning docker
Language:Python 58
anton-bushuiev / PPIRef
Dataset and package for working with protein-protein interactions in 3D
datasets machine-learning protein-protein-interaction proteins
Language:Jupyter Notebook 56
psipred / psipred
PSIPRED Protein Secondary Structure Predictor
secondary-structure-prediction proteins
Language:Java 50
sigven / oncoEnrichR
Cancer-dedicated gene set interpretation
cancer high-throughput-screening tcga-data report-generator protein-protein-interaction co-expression disease-gene-association crispr-target proteins genesets prioritization protein-complexes cancer-survival functional-enrichment-analysis tissue-enrichment-analysis pathway-enrichment-analysis cancer-hallmark-evidence
Language:R 48
Genentech / walk-jump
Official repository for discrete Walk-Jump Sampling (dWJS)
antibody machine-learning protein-design protein-sequences proteins
Language:Python 47
vsomnath / holoprot
Multi-Scale Representation Learning on Proteins (NeurIPS 2021)
geometry machine-learning neurips-2021 proteins representation-learning
Language:Python 46
mircare / Porter5
Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes
deep-learning hhblit machine-learning protein-structure-prediction proteins psi-blast secondary-structure
Language:C++ 44
BioinfoMachineLearning / DIPS-Plus
The Enhanced Database of Interacting Protein Structures for Interface Prediction
deep-learning bioinformatics datasets proteins machine-learning
Language:Python 42
OpenProteinAI / PoET
Inference code for PoET: A generative model of protein families as sequences-of-sequences
deep-learning generative-model protein-engineering protein-language-model protein-sequences proteins
Language:Python 42
prescient-design / walk-jump
Official repository for discrete Walk-Jump Sampling (dWJS)
antibody machine-learning protein-design protein-sequences proteins
Language:JavaScript 41
amazon-sagemaker-protein-classification
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.
protein-sequences protien-classification proteins amazon-sagemaker-studio amazon-sagemaker protbert-model bert-models sagemaker-distributed-data-parallel distributed-training
Language:Jupyter Notebook 40
anton-bushuiev / PPIformer
Learning to design protein-protein interactions with enhanced generalization (ICLR24)
equivariant-representations machine-learning protein-design protein-protein-interactions proteins
Language:Jupyter Notebook 39
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.
metabolomics-data peptides mass-spectrometry data-summarization proteins metabolites lipids rna-seq-analysis
Language:R 37
mims-harvard / PINNACLE
Contextualizing protein representations using deep learning on protein networks and single-cell data
context-aware contextual geometric-deep-learning graph-neural-networks proteins therapeutics
Language:Python 34
geometricus
TurtleTools / geometricus
A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.
proteins protein-structure invariant-features feature-engineering alignment-free machine-learning
Language:Jupyter Notebook 34