proteins

There are 6 repositories under proteins topic.

MolecularNodes
BradyAJohnston / MolecularNodes
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
biochemistry blender blender-addon geometry-nodes molecular molecular-dynamics molecular-graphics molecular-modeling molecule pdb protein protein-data-bank protein-structure protein-visualization proteins sciart structural-biology visualisation
Language:Python 1100
aqlaboratory / proteinnet
Standardized data set for machine learning of protein structure
dataset deep-learning machine-learning protein-sequence protein-structure proteins
Language:Python 904
microsoft / foldingdiff
Diffusion models of protein structure; trigonometry and attention are all you need!
diffusion diffusion-models protein proteins transformer protein-structure-generation
Language:Jupyter Notebook 557
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 518
p2rank
rdk / p2rank
P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.
bioinformatics machine-learning protein-structure pdb binding-sites proteins structural-bioinformatics java mmcif pymol groovy protein-ligand-docking molecular-structures drug-discovery virtual-screening p2rank chimerax protein-ligand-interactions docking ligand
Language:Groovy 356
williamgilpin / pypdb
A Python API for the RCSB Protein Data Bank (PDB)
blast pdb protein-data-bank protein-sequences protein-structure proteins proteomics
Language:Python 331
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 250
Acellera / moleculekit
MoleculeKit: Your favorite molecule manipulation kit
molecule machine-learning proteins drug-discovery molecular-modeling molecular-simulation
Language:Python 226
PDB-REDO / dssp
Application to assign secondary structure to proteins
dssp pdb proteins
Language:C++ 225
haddock3
haddocking / haddock3
Official repo of the modular BioExcel version of HADDOCK
bioinformatics complexes docking integrative-modeling modelling proteins utrecht-university workflows
Language:Python 200
biolib / openprotein
A PyTorch framework for prediction of tertiary protein structure
protein-structure proteins
Language:Python 190
mims-harvard / ATOMICA
Learning Universal Representations of Intermolecular Interactions with ATOMICA
atomistic-modelling geometric-deep-learning ions molecular-interactions molecular-structures nucleic-acids peptides proteins small-molecules
Language:Python 189
plass
soedinglab / plass
sensitive and precise assembly of short sequencing reads
bioinformatics metagenomics sequence-assembler proteins opensource proteomics metatranscriptomics
Language:C 161
saezlab / OmnipathR
R client for the OmniPath web service
omnipath complexes proteins enzyme-ptm pathways networks networks-biology
Language:R 147
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
140
BasedLabs / NoLabs
Open source biolab
ai bioinformatics folding webserver biolab proteins synthetic-biology protein-design
Language:JavaScript 134
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 128
Genentech / equifold
Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
machine-learning proteins structural-biology structure-prediction
Language:Python 124
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 120
lucidrains / progen
Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax
artificial-intelligence deep-learning proteins
Language:Python 113
samirelanduk / atomium
Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)
biology proteins structural-biology chemistry molecules
Language:Python 106
anton-bushuiev / PPIRef
Dataset and package for working with protein-protein interactions in 3D
datasets machine-learning protein-protein-interaction proteins
Language:Jupyter Notebook 96
mims-harvard / PINNACLE
Contextual AI models for single-cell protein biology
context-aware contextual geometric-deep-learning graph-neural-networks proteins therapeutics
Language:Python 89
diegozea / MIToS.jl
A Julia package to analyze protein sequences, structures, and evolutionary information
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 83
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 80
DeepInteract
BioinfoMachineLearning / DeepInteract
A geometric deep learning framework (Geometric Transformers) for predicting protein interface contacts. (ICLR 2022)
bioinformatics deep-learning docker geometric-deep-learning graph-neural-networks machine-learning protein-protein-interactions proteins transformers
Language:Python 64
prescient-design / walk-jump
Official repository for discrete Walk-Jump Sampling (dWJS)
antibody machine-learning protein-design protein-sequences proteins
Language:JavaScript 58
psipred / psipred
PSIPRED Protein Secondary Structure Predictor
proteins secondary-structure-prediction
Language:Java 58
Genentech / walk-jump
Official repository for discrete Walk-Jump Sampling (dWJS)
antibody machine-learning protein-design protein-sequences proteins
Language:Python 53
sigven / oncoEnrichR
Explore the cancer relevance of your gene list
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 52
BioinfoMachineLearning / DIPS-Plus
The Enhanced Database of Interacting Protein Structures for Interface Prediction
bioinformatics datasets deep-learning machine-learning proteins
Language:Python 50
anton-bushuiev / PPIformer
Learning to design protein-protein interactions with enhanced generalization (ICLR 2024)
equivariant-representations machine-learning protein-design protein-protein-interactions proteins
Language:Jupyter Notebook 49
vsomnath / holoprot
Multi-Scale Representation Learning on Proteins (NeurIPS 2021)
neurips-2021 machine-learning proteins geometry representation-learning
Language:Python 48
HySonLab / Directed_Evolution
Protein Design by Machine Learning guided Directed Evolution
directed-evolution large-language-models protein-design proteins
Language:Python 46
mircare / Porter5
Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes
proteins machine-learning deep-learning secondary-structure hhblit psi-blast protein-structure-prediction
Language:C++ 46
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 46