34 results found Sort:

aqlaboratory
proteinnet aqlaboratory
131
850
mit
54
Standardized data set for machine learning of protein structure
dataset proteins deep-learning machine-learning protein-sequence protein-structure
Created 2018-03-10
192 commits to master branch, last one 3 years ago
BradyAJohnston
MolecularNodes BradyAJohnston
81
825
mit
16
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
pdb sciart blender protein molecule proteins biochemistry blender-addon visualisation geometry-nodes protein-data-bank protein-structure molecular-modeling structural-biology protein-visualization
Created 2022-04-25
1,560 commits to main branch, last one 16 days ago
microsoft
foldingdiff microsoft
50
484
mit
20
Diffusion models of protein structure; trigonometry and attention are all you need!
protein proteins diffusion transformer diffusion-models protein-structure-generation
Created 2022-06-30
979 commits to main branch, last one 6 months ago
HannesStark
EquiBind HannesStark
110
464
mit
9
EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
geometry proteins molecules equivariance drug-discovery protein-structure graph-neural-networks
Created 2021-10-26
36 commits to main branch, last one about a year ago
williamgilpin
pypdb williamgilpin
77
300
mit
20
A Python API for the RCSB Protein Data Bank (PDB)
pdb blast proteins proteomics protein-data-bank protein-sequences protein-structure
Created 2015-05-13
176 commits to master branch, last one about a month ago
rdk
p2rank rdk
32
230
mit
9
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.
pdb java mmcif pymol groovy ligand p2rank proteins binding-sites random-forest bioinformatics drug-discovery protein-surface machine-learning protein-structure virtual-screening molecular-structures protein-ligand-docking structural-bioinformatics protein-ligand-interactions
Created 2016-09-25
1,591 commits to develop branch, last one 23 hours ago
octavian-ganea
equidock_public octavian-ganea
57
226
mit
8
EquiDock: geometric deep learning for fast rigid 3D protein-protein docking
docking geometry proteins deeplearning equivariance drugdiscovery drug-discovery graphneuralnetwork equivariant-network equivariant-representations protein-protein-interaction
Created 2022-02-04
20 commits to main branch, last one 2 years ago
Acellera
moleculekit Acellera
35
193
other
11
MoleculeKit: Your favorite molecule manipulation kit
molecule proteins drug-discovery machine-learning molecular-modeling molecular-simulation
Created 2019-03-28
880 commits to main branch, last one a day ago
biolib
openprotein biolib
55
178
mit
10
A PyTorch framework for prediction of tertiary protein structure
proteins protein-structure
Created 2018-09-08
163 commits to master branch, last one 4 years ago
PDB-REDO
dssp PDB-REDO
18
145
bsd-2-clause
5
Application to assign secondary structure to proteins
pdb dssp proteins
Created 2020-09-22
295 commits to trunk branch, last one 2 months ago
soedinglab
plass soedinglab
14
130
gpl-3.0
10
sensitive and precise assembly of short sequencing reads
proteins opensource proteomics metagenomics bioinformatics sequence-assembler metatranscriptomics
Created 2018-01-19
3,797 commits to master branch, last one 14 days ago
Genentech
equifold Genentech
15
117
apache-2.0
10
Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
proteins machine-learning structural-biology structure-prediction
Created 2022-11-29
15 commits to main branch, last one about a year ago
lucidrains
progen lucidrains
17
108
mit
8
Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax
proteins deep-learning artificial-intelligence
Created 2021-06-09
90 commits to main branch, last one 2 years ago
chao1224
Geom3D chao1224
9
105
mit
2
Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023
3d drugs group biology physics crystals geometry material proteins symmetry chemistry molecules ai4science invariance equivariance 3d-structures
Created 2023-06-07
9 commits to main branch, last one 10 months ago
samirelanduk
atomium samirelanduk
20
101
mit
6
Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)
biology proteins chemistry molecules structural-biology
Created 2016-05-04
1,301 commits to master branch, last one 2 years ago
saezlab
OmnipathR saezlab
19
94
mit
10
R client for the OmniPath web service
networks omnipath pathways proteins complexes enzyme-ptm networks-biology
Created 2018-11-09
1,430 commits to master branch, last one 13 days ago
virtualramblas
awesome-deep-learning-4-life-sciences virtualramblas
11
92
apache-2.0
6
A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).
python biotech proteins molecules deeplearning drug-discovery cheminformatics pharmaceuticals drug-repurposing
Created 2022-06-24
123 commits to main branch, last one 3 months ago
haddocking
haddock3 haddocking
28
84
apache-2.0
17
Official repo of the modular BioExcel version of HADDOCK
docking python3 proteins complexes modelling workflows bioinformatics utrecht-university integrative-modeling
Created 2019-03-13
3,374 commits to main branch, last one 23 hours ago
BasedLabs
NoLabs BasedLabs
4
75
apache-2.0
3
Open source biolab
ai biolab folding proteins webserver bioinformatics synthetic-biology
Created 2023-05-27
768 commits to master branch, last one a day ago
diegozea
MIToS.jl diegozea
18
65
other
2
Mutual Information Tools for protein Sequence analysis in Julia
pdb pfam sifts biology proteins coevolution conservation bioinformatics julia-language protein-evolution protein-structure mutual-information protein-sequence-analysis structural-bioinformatics multiple-sequence-alignment
Created 2015-06-18
822 commits to master branch, last one 19 hours ago
BioinfoMachineLearning
DeepInteract BioinfoMachineLearning
11
58
gpl-3.0
2
A geometric deep learning pipeline for predicting protein interface contacts. (ICLR 2022)
docker proteins transformers deep-learning bioinformatics machine-learning graph-neural-networks geometric-deep-learning protein-protein-interactions
Created 2021-10-04
58 commits to main branch, last one 2 years ago
anton-bushuiev
PPIRef anton-bushuiev
5
53
mit
3
Dataset and package for working with protein-protein interactions in 3D
datasets proteins machine-learning protein-protein-interaction
Created 2023-10-16
86 commits to main branch, last one a day ago
psipred
psipred psipred
10
50
other
5
PSIPRED Protein Secondary Structure Predictor
proteins secondary-structure-prediction
Created 2015-11-03
13 commits to master branch, last one 5 years ago
sigven
oncoEnrichR sigven
10
48
mit
7
Cancer-dedicated gene set interpretation
cancer genesets proteins tcga-data co-expression crispr-target prioritization cancer-survival report-generator protein-complexes cancer-hallmark-evidence disease-gene-association high-throughput-screening tissue-enrichment-analysis pathway-enrichment-analysis protein-protein-interaction functional-enrichment-analysis
Created 2019-11-21
307 commits to master branch, last one 10 months ago
Genentech
walk-jump Genentech
8
47
apache-2.0
6
Official repository for discrete Walk-Jump Sampling (dWJS)
antibody proteins protein-design machine-learning protein-sequences
Created 2023-05-26
35 commits to main branch, last one 10 months ago
vsomnath
holoprot vsomnath
8
46
mit
2
Multi-Scale Representation Learning on Proteins (NeurIPS 2021)
geometry proteins neurips-2021 machine-learning representation-learning
Created 2022-01-04
8 commits to main branch, last one 12 months ago
BioinfoMachineLearning
DIPS-Plus BioinfoMachineLearning
8
42
gpl-3.0
1
The Enhanced Database of Interacting Protein Structures for Interface Prediction
datasets proteins deep-learning bioinformatics machine-learning
Created 2021-05-27
117 commits to main branch, last one 9 months ago
OpenProteinAI
PoET OpenProteinAI
2
40
mit
3
Inference code for PoET: A generative model of protein families as sequences-of-sequences
proteins deep-learning generative-model protein-sequences protein-engineering protein-language-model
Created 2023-10-28
8 commits to main branch, last one 2 months ago
aws-samples
amazon-sagemaker-protein-classification aws-samples
22
40
mit-0
29
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 corp...
proteins bert-models protbert-model amazon-sagemaker protein-sequences distributed-training protien-classification amazon-sagemaker-studio sagemaker-distributed-data-parallel
Created 2021-01-01
17 commits to main branch, last one 2 years ago
prescient-design
walk-jump prescient-design
5
40
apache-2.0
5
Official repository for discrete Walk-Jump Sampling (dWJS)
antibody proteins protein-design machine-learning protein-sequences
Created 2023-08-14
11 commits to main branch, last one 23 days ago