33 results found Sort:

Peldom
papers_for_protein_design_using_DL Peldom
174
1.5k
gpl-3.0
116
List of papers about Proteins Design using Deep Learning
deep-learning protein-design
Created 2021-11-25
301 commits to main branch, last one 6 days ago
a-r-j
graphein a-r-j
132
1.0k
mit
18
Protein Graph Library
dgl rna python protein pytorch interactome ppi-networks deep-learning interactomics bioinformatics drug-discovery protein-design protein-data-bank protein-structure pytorch-geometric structural-biology computational-biology graph-neural-networks geometric-deep-learning gene-regulatory-networks
Created 2019-08-28
807 commits to master branch, last one 29 days ago
PaddlePaddle
PaddleHelix PaddlePaddle
225
1.0k
other
24
Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集
ddi dti ppi biocomputing deeplearning graph-networks protein-design molecule-design protein-docking protein-folding machine-learning representation-learning rna-structure-prediction self-supervised-learning protein-structure-prediction
Created 2020-11-21
864 commits to dev branch, last one 6 days ago
RosettaCommons
PyRosetta.notebooks RosettaCommons
151
491
mit
329
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
dna rosetta pyrosetta google-colab protein-design protein-docking protein-folding jupyter-notebook rna-structure-prediction protein-structure-prediction
Created 2019-05-24
595 commits to master branch, last one 3 months ago
lightdock
lightdock lightdock
42
307
gpl-3.0
12
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
dna docking protein peptides chemistry proteomics bioinformatics protein-design protein-docking molecular-biology protein-structure structural-biology swarm-intelligence bioinformatics-tool molecular-structures artificial-intelligence protein-dna-interactions structural-bioinformatics glowworm-swarm-optimization protein-protein-interaction
Created 2019-09-27
488 commits to master branch, last one 10 months ago
adaptyvbio
ProteinFlow adaptyvbio
17
242
bsd-3-clause
8
Versatile computational pipeline for processing protein structure data for deep learning applications.
dataset deep-learning bioinformatics protein-design protein-data-bank protein-structure
Created 2023-02-15
1,309 commits to main branch, last one 9 months ago
OATML-Markslab
ProteinGym OATML-Markslab
25
241
mit
6
Official repository for the ProteinGym benchmarks
protein benchmark protein-design protein-fitness computational-biology
Created 2022-12-15
93 commits to main branch, last one 19 days ago
RosettaCommons
rosetta RosettaCommons
67
171
other
199
The Rosetta Bio-macromolecule modeling package.
enzyme-design protein-design antibody-design protein-structure macromolecular-modeling
Created 2023-11-17
11,691 commits to main branch, last one 8 days ago
aqlaboratory
genie aqlaboratory
20
168
apache-2.0
6
De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds
protein-design diffusion-models
Created 2022-12-07
16 commits to main branch, last one 7 months ago
lucidrains
chroma-pytorch lucidrains
23
158
mit
19
Implementation of Chroma, generative models of protein using DDPM and GNNs, in Pytorch
deep-learning protein-design denoising-diffusion graph-neural-networks artificial-intelligence
Created 2022-12-02
12 commits to main branch, last one about a year ago
samsinai
FLEXS samsinai
21
156
apache-2.0
9
Fitness landscape exploration sandbox for biological sequence design.
benchmarking deep-learning protein-design machine-learning bayesian-optimization computational-biology deep-reinforcement-learning
Created 2019-12-02
505 commits to master branch, last one 2 years ago
J-SNACKKB
FLIP J-SNACKKB
14
94
afl-3.0
7
A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design
protein protein-design protein-sequences representation-learning protein-fitness-prediction protein-function-prediction
Created 2021-05-13
178 commits to main branch, last one 3 months ago
lightonai
RITA lightonai
8
94
mit
6
RITA is a family of autoregressive protein models, developed by LightOn in collaboration with the OATML group at Oxford and the Debora Marks Lab at Harvard.
deep-learning protein-design generative-models
Created 2022-05-06
24 commits to master branch, last one about a year ago
OATML-Markslab
ProteinNPT OATML-Markslab
8
83
mit
1
Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"
protein-design
Created 2023-10-28
55 commits to master branch, last one 14 days ago
lucidrains
tr-rosetta-pytorch lucidrains
10
80
mit
4
Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design
deep-learning protein-design protein-folding artificial-intelligence
Created 2021-02-04
22 commits to main branch, last one 3 years ago
Eikor
InstructPLM Eikor
5
71
apache-2.0
2
The first large protein language model trained follows structure instructions.
pytorch huggingface protein-design
Created 2024-03-31
24 commits to main branch, last one 5 months ago
westlake-repl
SaprotHub westlake-repl
7
69
mit
4
SaprotHub: Making Protein Modeling Accessible to All Biologists
nlp saprot saprothub protein-design protein-fitness universal-model foundation-models protein-structure protein-language-model protein-function-prediction protein-protein-interaction
Created 2024-05-02
437 commits to main branch, last one 9 days ago
samuelstanton
lambo samuelstanton
22
66
apache-2.0
4
Code to reproduce experiments in "Accelerating Bayesian Optimization for Protein Design with Denoising Autoencoders" (Stanton et al 2022)
protein-design bayesian-optimization
Created 2022-03-14
62 commits to main branch, last one 7 months ago
lucidrains
equiformer-diffusion lucidrains
4
56
mit
12
Implementation of Denoising Diffusion for protein design, but using the new Equiformer (successor to SE3 Transformers) with some additional improvements
deep-learning protein-design denoising-diffusion attention-mechanisms equivariant-networks artificial-intelligence
Created 2022-12-27
2 commits to main branch, last one about a year ago
ostrokach
proteinsolver ostrokach
8
54
mit
2
Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.
protein bioinformatics protein-design protein-sequence protein-structure structural-biology graph-neural-networks
Created 2020-04-08
406 commits to master branch, last one 3 years ago
wells-wood-research
timed-design wells-wood-research
11
50
unknown
4
Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis
protein protein-design
Created 2021-11-13
348 commits to main branch, last one 2 months ago
Genentech
walk-jump Genentech
8
49
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 about a year ago
timkartar
DeepPBS timkartar
6
49
bsd-3-clause
5
Geometric deep learning of protein–DNA binding specificity
p53 python pytorch protein-dna protein-design pytorch-geometric binding-specificity geometric-deep-learning molecular-dynamics-simulation
Created 2023-04-20
110 commits to main branch, last one about a month ago
prescient-design
walk-jump prescient-design
5
45
apache-2.0
6
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 5 months ago
anton-bushuiev
PPIformer anton-bushuiev
4
44
mit
5
Learning to design protein-protein interactions with enhanced generalization (ICLR 2024)
proteins protein-design machine-learning equivariant-representations protein-protein-interactions
Created 2023-10-05
27 commits to main branch, last one 28 days ago
chao1224
ProteinDT chao1224
4
43
mit
6
A Text-guided Protein Design Framework, Nat Mach Intell 2024
llm protein ai4science drug-design protein-design protein-editing foundation-model protein-sequence protein-structure large-language-model
Created 2023-02-05
5 commits to main branch, last one 4 months ago
HySonLab
Protein_Redesign HySonLab
5
39
mit
4
Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models
protein ligand-binding protein-design diffusion-models equivariant-network protein-representation-learning
Created 2024-02-13
23 commits to main branch, last one 11 days ago
EDAPINENUT
GeoAB EDAPINENUT
10
36
unknown
2
This is the official repository of paper - GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation (ICML2024)
generative-ai protein-design antibody-design protein-structure
Created 2024-03-23
15 commits to main branch, last one 5 months ago
LBM-EPFL
CARBonAra LBM-EPFL
6
34
other
1
Deep learning framework for protein sequence design from a backbone scaffold that can leverage the molecular context including non-protein entities.
pytorch deep-learning protein-design protein-structure geometric-deep-learning
Created 2023-06-09
25 commits to main branch, last one 6 months ago
XinshaoAmosWang
DeepCriticalLearning XinshaoAmosWang
4
31
other
2
Deep Critical Learning. Implementation of ProSelfLC, IMAE, DM, etc.
pytorch deep-learning protein-design bert-transformer protein-transformer image-classification protein-localization protein-classification protein-function-prediction convolutional-neural-networks
Created 2022-08-06
30 commits to master branch, last one about a year ago