protein

There are 20 repositories under protein topic.

biopython / biopython
Official git repository for Biopython (originally converted from CVS)
bioinformatics biopython dna genomics phylogenetics protein protein-structure python sequence-alignment
Language:Python 4194
graphein
a-r-j / graphein
Protein Graph Library
protein protein-structure deep-learning pytorch graph-neural-networks dgl computational-biology bioinformatics structural-biology protein-data-bank protein-design geometric-deep-learning pytorch-geometric python interactomics interactome rna ppi-networks gene-regulatory-networks drug-discovery
Language:Jupyter Notebook 989
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 800
salesforce / progen
Official release of the ProGen models
generative-model language-model protein
Language:Python 572
flowhub-team / awesome-omics
A collection of awesome things regarding all omics.
genomics protein single-cell ngs ngs-pipeline wgs-analysis awesome omics
543
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 467
mdshw5 / pyfaidx
Efficient pythonic random access to fasta subsequences
python bioinformatics fasta indexing dna protein genomics bgzf samtools
Language:Python 442
prody / ProDy
A Python Package for Protein Dynamics Analysis
python protein dynamics
Language:Python 393
haddocking / pdb-tools
A dependency-free cross-platform swiss army knife for PDB files.
python protein pdb bioinformatics structural-biology structural-bioinformatics rcsb utrecht-university
Language:Python 364
lightdock
lightdock / lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
protein protein-structure protein-protein-interaction protein-docking swarm-intelligence glowworm-swarm-optimization protein-dna-interactions peptides dna docking artificial-intelligence protein-design proteomics structural-biology structural-bioinformatics bioinformatics bioinformatics-tool chemistry molecular-biology molecular-structures
Language:Python 278
AngelRuizMoreno / Jupyter_Dock
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.
molecular-docking autodock autodock-vina ledock mdanalysis rdkit openbabel cheminformatics computational-biology jupyter-notebook py3dmol protein protein-structure drug-discovery drug-repurposing drug-design
Language:Jupyter Notebook 246
fogleman / ribbon
Ribbon diagrams of proteins in #golang.
3d biochemistry chemistry go protein protein-data-bank
Language:Go 243
westlake-repl / SaProt
Saprot: Protein Language Model with Structural Alphabet
alphafold2 foldseek predicted-structures pretraining protein protein-language-model protein-llm protein-sequence protein-structure representation-learning structural-alphbet structure-aware
Language:Python 226
seqviz
Lattice-Automation / seqviz
a JavaScript DNA, RNA, and protein sequence viewer
biology dna igem plasmid protein rna synthetic-biology vector
Language:TypeScript 219
debbiemarkslab / EVcouplings
Evolutionary couplings from protein and RNA sequence alignments
structure-prediction 3d-structure protein protein-complexes
Language:Jupyter Notebook 213
zjunlp / Mol-Instructions
[ICLR 2024] Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models
ai-for-science biomedical dataset datasets generation iclr2024 instruction instruction-following instructions large-language-models llama mol-instruction molecule natural-language-processing protein resource science
Language:Python 198
opendilab / awesome-AI-based-protein-design
A collection of research papers for AI-based protein design
artificial-intelligence awesome awesome-list protein protein-structure
187
PeptoneLtd / dspp-keras
Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.
protein protein-structure biology biotechnology machine-learning ai tensorflow keras amino-acids polymer dataset database prediction
Language:Python 166
a-r-j / ProteinWorkshop
Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)
benchmark dataset deep-learning lightning pretraining protein protein-structure pytorch
Language:Python 155
HICAI-ZJU / Scientific-LLM-Survey
Scientific Large Language Models: A Survey on Biological & Chemical Domains
cell genome llms molecule multimodal protein sci-llm science-research scientific-languages text
144
ncbi / icn3d
web-based protein structure viewer and analysis tool interactively or in batch mode
icn3d webgl protein 3d-structure 3d-viewer structure-viewer nucleotide chemical protein-viewer jupyter-notebook snp delphi nodejs molecular-viewer ar vr
Language:JavaScript 144
zjunlp / OntoProtein
[ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding
protein-protein-interaction gene-ontology protein-pretraining protein-function-prediction protein-structure-prediction knowledge-graph protein ontoprotein bert nlp pytorch pretrained-models pretraining iclr iclr2022
Language:Python 135
Shen-Lab / DeepAffinity
Protein-compound affinity prediction through unified RNN-CNN
drug-discovery interpretable-deep-learning semi-supervised-learning attention-mechanism protein
Language:Python 134
beautiful-atoms / beautiful-atoms
Python module for drawing and rendering beautiful atoms and molecules using Blender.
3d ase atomic atoms blender crystal molecule protein pymatgen python rendering ribbon-diagram
Language:Python 124
biologyguy / BuddySuite
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
bioinformatics python phylogenetics dna protein alignment command-line workflow biology
Language:Python 122
chao1224 / ChatDrug
LLM for Drug Editing, ICLR 2024
chatgpt conversation drug drug-discovery editing molecule motif peptide protein retrieval secondary-structure small-molecule structure domain-feedback drug-editing chatgpt3 llm
Language:Python 122
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
DeepRank / Deeprank-GNN
Graph Network for protein-protein interface
graph protein graph-networks interface-classification protein-protein-interactions pssm scoring utrecht-university
Language:Python 115
Rostlab / SeqVec
Modelling the Language of Life - Deep Learning Protein Sequences
protein bioinformatics protein-structure protein-function
Language:Python 112
malllabiisc / ProteinGCN
ProteinGCN: Protein model quality assessment using Graph Convolutional Networks
deep-learning graph-convolutional-networks graph-neural-networks protein protein-model-quality-estimation pytorch
Language:Python 109
jgreener64 / mmterm
View proteins and trajectories in the terminal
protein protein-structure terminal terminal-graphics trajectory visualization
Language:Python 103
flatironinstitute / deepblast
Neural Networks for Protein Sequence Alignment
structural-alignments neural-networks sequence-alignment language-modeling protein-sequences protein protein-structure
Language:Python 100
molstar / VSCoding-Sequence
VSCode Extension for interactively visualising protein structure data in the editor
molecule molstar pdb pdb-files protein protein-structure structural-biology structure vscode vscode-extension
Language:TypeScript 92
swsoyee / r3dmol
🧬 An R package for visualizing molecular data in 3D
protein protein-structure 3d r htmlwidgets visualization molecular-graphics molecular-modeling computational-biology computational-chemistry hacktoberfest
Language:JavaScript 88
J-SNACKKB / FLIP
A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design
protein protein-sequences protein-design representation-learning protein-fitness-prediction protein-function-prediction
Language:Jupyter Notebook 84
food-nutrients / food-nutrients
:fork_and_knife: Food Nutrients
food food-recommendation food-classification nutrition nutrients vitamins protein carbs fat minerals essential foods
Language:JavaScript 80