67 results found Sort:

biopython
biopython biopython
1.8k
4.4k
other
168
Official git repository for Biopython (originally converted from CVS)
dna python protein genomics biopython phylogenetics bioinformatics protein-structure sequence-alignment
Created 2009-03-15
15,956 commits to master branch, last one a day 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 28 days ago
BradyAJohnston
MolecularNodes BradyAJohnston
87
916
gpl-3.0
19
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
pdb sciart blender protein molecule proteins molecular biochemistry blender-addon visualisation geometry-nodes protein-data-bank protein-structure molecular-dynamics molecular-graphics molecular-modeling structural-biology protein-visualization
Created 2022-04-25
1,739 commits to main branch, last one 10 days ago
salesforce
progen salesforce
115
623
bsd-3-clause
20
Official release of the ProGen models
protein language-model generative-model
Created 2022-05-16
66 commits to main branch, last one 2 years ago
flowhub-team
awesome-omics flowhub-team
66
549
mit
35
A collection of awesome things regarding all omics.
ngs omics awesome protein genomics single-cell ngs-pipeline wgs-analysis
Created 2022-02-15
216 commits to main branch, last one 10 months ago
microsoft
foldingdiff microsoft
59
519
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 11 months ago
mdshw5
pyfaidx mdshw5
75
460
other
9
Efficient pythonic random access to fasta subsequences
dna bgzf fasta python protein genomics indexing samtools bioinformatics
Created 2013-09-12
879 commits to master branch, last one about a month ago
prody
ProDy prody
157
435
other
25
A Python Package for Protein Dynamics Analysis
python protein dynamics
Created 2010-10-31
9,371 commits to main branch, last one 2 hours ago
haddocking
pdb-tools haddocking
114
389
apache-2.0
14
A dependency-free cross-platform swiss army knife for PDB files.
pdb rcsb python protein bioinformatics structural-biology utrecht-university structural-bioinformatics
Created 2014-11-27
478 commits to master branch, last one 11 months ago
westlake-repl
SaProt westlake-repl
33
354
mit
6
Saprot: Protein Language Model with Structural Alphabet (AA+3Di)
protein foldseek alphafold2 pretraining protein-llm structure-aware protein-sequence protein-structure structural-alphbet predicted-structures protein-language-model representation-learning
Created 2023-10-02
124 commits to main branch, last one 2 days 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
martinpacesa
BindCraft martinpacesa
60
298
mit
11
User friendly and accurate binder design pipeline
binder design protein pyrosetta alphafold2
Created 2024-09-18
51 commits to main branch, last one 11 days ago
AngelRuizMoreno
Jupyter_Dock AngelRuizMoreno
67
259
mit
12
Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
rdkit ledock protein py3dmol autodock openbabel mdanalysis drug-design autodock-vina drug-discovery cheminformatics drug-repurposing jupyter-notebook molecular-docking protein-structure computational-biology
Created 2021-09-10
29 commits to main branch, last one 2 years ago
zjunlp
Mol-Instructions zjunlp
16
252
mit
7
[ICLR 2024] Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models
llama dataset protein science datasets iclr2024 molecule resource biomedical generation instruction instructions ai-for-science mol-instruction instruction-following large-language-models natural-language-processing
Created 2023-04-12
210 commits to main branch, last one 23 days ago
Lattice-Automation
seqviz Lattice-Automation
53
246
mit
13
a JavaScript DNA, RNA, and protein sequence viewer
dna rna igem vector biology plasmid protein synthetic-biology
Created 2019-04-24
767 commits to develop branch, last one 21 days ago
HICAI-ZJU
Scientific-LLM-Survey HICAI-ZJU
22
246
unknown
7
Scientific Large Language Models: A Survey on Biological & Chemical Domains
cell llms text genome survey protein sci-llm molecule multimodal science-research scientific-languages large-language-models
Created 2023-10-12
37 commits to main branch, last one 4 months ago
fogleman
ribbon fogleman
24
243
mit
11
Ribbon diagrams of proteins in #golang.
3d go protein chemistry biochemistry protein-data-bank
Created 2017-02-21
17 commits to master branch, last one 5 years ago
debbiemarkslab
EVcouplings debbiemarkslab
76
241
other
25
Evolutionary couplings from protein and RNA sequence alignments
protein 3d-structure protein-complexes structure-prediction
Created 2016-07-20
1,155 commits to develop branch, last one 7 days 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
opendilab
awesome-AI-based-protein-design opendilab
14
229
apache-2.0
3
A collection of research papers for AI-based protein design
awesome protein awesome-list protein-structure artificial-intelligence
Created 2022-11-07
14 commits to main branch, last one 6 months ago
a-r-j
ProteinWorkshop a-r-j
16
202
mit
7
Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)
dataset protein pytorch benchmark lightning pretraining deep-learning protein-structure
Created 2023-05-17
248 commits to main branch, last one 7 months ago
PeptoneLtd
dspp-keras PeptoneLtd
21
169
agpl-3.0
14
Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.
ai keras biology dataset polymer protein database prediction tensorflow amino-acids biotechnology machine-learning protein-structure
Created 2017-05-24
76 commits to master branch, last one 7 years ago
ncbi
icn3d ncbi
42
154
other
19
web-based protein structure viewer and analysis tool interactively or in batch mode
ar vr snp icn3d webgl delphi nodejs protein chemical 3d-viewer nucleotide 3d-structure protein-viewer jupyter-notebook molecular-viewer structure-viewer
Created 2016-01-20
1,492 commits to master branch, last one 4 days ago
zjunlp
OntoProtein zjunlp
22
144
mit
7
[ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding
nlp bert iclr protein pytorch iclr2022 ontoprotein pretraining gene-ontology knowledge-graph pretrained-models protein-pretraining protein-function-prediction protein-protein-interaction protein-structure-prediction
Created 2021-12-18
51 commits to main branch, last one about a year ago
beautiful-atoms
beautiful-atoms beautiful-atoms
25
143
gpl-3.0
3
Python module for drawing and rendering beautiful atoms and molecules using Blender.
3d ase atoms atomic python blender crystal protein molecule pymatgen rendering ribbon-diagram
Created 2021-10-15
927 commits to main branch, last one 6 months ago
chao1224
ChatDrug chao1224
8
141
unknown
3
LLM for Drug Editing, ICLR 2024
llm drug motif chatgpt editing peptide protein chatgpt3 molecule retrieval structure conversation drug-editing drug-discovery small-molecule domain-feedback secondary-structure
Created 2023-05-18
27 commits to main branch, last one 5 months ago
Shen-Lab
DeepAffinity Shen-Lab
30
137
gpl-3.0
9
Protein-compound affinity prediction through unified RNN-CNN
protein drug-discovery attention-mechanism semi-supervised-learning interpretable-deep-learning
Created 2018-05-22
76 commits to master branch, last one 4 months ago
biologyguy
BuddySuite biologyguy
23
124
other
13
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
dna python biology protein workflow alignment command-line phylogenetics bioinformatics
Created 2015-01-15
1,989 commits to master branch, last one 2 years ago
DeepRank
Deeprank-GNN DeepRank
32
117
apache-2.0
7
Graph Network for protein-protein interface
pssm graph protein scoring graph-networks utrecht-university interface-classification protein-protein-interactions
This repository has been archived (exclude archived)
Created 2018-07-13
590 commits to master branch, last one 8 months ago
malllabiisc
ProteinGCN malllabiisc
18
115
apache-2.0
6
ProteinGCN: Protein model quality assessment using Graph Convolutional Networks
protein pytorch deep-learning graph-neural-networks graph-convolutional-networks protein-model-quality-estimation
Created 2019-05-06
23 commits to master branch, last one 4 years ago