Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists tagged with protein
A curated list of projects in awesome lists tagged with protein .
https://github.com/biopython/biopython
Official git repository for Biopython (originally converted from CVS)
bioinformatics biopython dna genomics phylogenetics protein protein-structure python sequence-alignment
Last synced: 29 Sep 2024
https://github.com/a-r-j/graphein
Protein Graph Library
bioinformatics computational-biology deep-learning dgl drug-discovery gene-regulatory-networks geometric-deep-learning graph-neural-networks interactome interactomics ppi-networks protein protein-data-bank protein-design protein-structure python pytorch pytorch-geometric rna structural-biology
Last synced: 02 Aug 2024
https://github.com/BradyAJohnston/MolecularNodes
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
biochemistry blender blender-addon geometry-nodes molecular-modeling molecule pdb protein protein-data-bank protein-structure protein-visualization proteins sciart structural-biology visualisation
Last synced: 02 Aug 2024
https://github.com/bradyajohnston/molecularnodes
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
biochemistry blender blender-addon geometry-nodes molecular-modeling molecule pdb protein protein-data-bank protein-structure protein-visualization proteins sciart structural-biology visualisation
Last synced: 26 Sep 2024
https://github.com/microsoft/foldingdiff
Diffusion models of protein structure; trigonometry and attention are all you need!
diffusion diffusion-models protein protein-structure-generation proteins transformer
Last synced: 01 Aug 2024
https://github.com/mdshw5/pyfaidx
Efficient pythonic random access to fasta subsequences
bgzf bioinformatics dna fasta genomics indexing protein python samtools
Last synced: 02 Aug 2024
https://github.com/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.
autodock autodock-vina cheminformatics computational-biology drug-design drug-discovery drug-repurposing jupyter-notebook ledock mdanalysis molecular-docking openbabel protein protein-structure py3dmol rdkit
Last synced: 09 Aug 2024
https://github.com/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
Last synced: 26 Sep 2024
https://github.com/hicai-zju/scientific-llm-survey
Scientific Large Language Models: A Survey on Biological & Chemical Domains
cell genome large-language-models llms molecule multimodal protein sci-llm science-research scientific-languages survey text
Last synced: 26 Sep 2024
https://github.com/HICAI-ZJU/Scientific-LLM-Survey?tab=readme-ov-file
Scientific Large Language Models: A Survey on Biological & Chemical Domains
cell genome large-language-models llms molecule multimodal protein sci-llm science-research scientific-languages survey text
Last synced: 02 Aug 2024
https://github.com/peptoneltd/dspp-keras
Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.
ai amino-acids biology biotechnology database dataset keras machine-learning polymer prediction protein protein-structure tensorflow
Last synced: 26 Sep 2024
https://github.com/ncbi/icn3d
web-based protein structure viewer and analysis tool interactively or in batch mode
3d-structure 3d-viewer ar chemical delphi icn3d jupyter-notebook molecular-viewer nodejs nucleotide protein protein-viewer snp structure-viewer vr webgl
Last synced: 30 Sep 2024
https://github.com/zjunlp/OntoProtein
[ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding
bert gene-ontology iclr iclr2022 knowledge-graph nlp ontoprotein pretrained-models pretraining protein protein-function-prediction protein-pretraining protein-protein-interaction protein-structure-prediction pytorch
Last synced: 08 Aug 2024
https://github.com/chao1224/chatdrug
LLM for Drug Editing, ICLR 2024
chatgpt chatgpt3 conversation domain-feedback drug drug-discovery drug-editing editing llm molecule motif peptide protein retrieval secondary-structure small-molecule structure
Last synced: 26 Sep 2024
https://github.com/Shen-Lab/DeepAffinity
Protein-compound affinity prediction through unified RNN-CNN
attention-mechanism drug-discovery interpretable-deep-learning protein semi-supervised-learning
Last synced: 03 Aug 2024
https://github.com/chao1224/ChatDrug
LLM for Drug Editing, ICLR 2024
chatgpt chatgpt3 conversation domain-feedback drug drug-discovery drug-editing editing llm molecule motif peptide protein retrieval secondary-structure small-molecule structure
Last synced: 03 Aug 2024
https://github.com/bio4j/bio4j
Bio4j abstract model and general entry point to the project
bio4j bio4j-titan bioinformatics database gene-ontology graph graph-data graph-database graph-databases graph-queries graph-schema java java-8 ncbi-taxonomy property-graph protein proteins titan uniprot uniref
Last synced: 28 Sep 2024
https://github.com/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
Last synced: 26 Sep 2024
https://github.com/flatironinstitute/deepblast
Neural Networks for Protein Sequence Alignment
language-modeling neural-networks protein protein-sequences protein-structure sequence-alignment structural-alignments
Last synced: 02 Aug 2024
https://github.com/swsoyee/r3dmol
🧬 An R package for visualizing molecular data in 3D
3d computational-biology computational-chemistry hacktoberfest htmlwidgets molecular-graphics molecular-modeling protein protein-structure r visualization
Last synced: 03 Aug 2024
https://github.com/food-nutrients/food-nutrients
:fork_and_knife: Food Nutrients
carbs essential fat food food-classification food-recommendation foods minerals nutrients nutrition protein vitamins
Last synced: 01 Aug 2024
https://github.com/ostrokach/proteinsolver
Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.
bioinformatics graph-neural-networks protein protein-design protein-sequence protein-structure structural-biology
Last synced: 02 Aug 2024
https://github.com/gersteinlab/genai4drug
drug-discovery genai molecule protein
Last synced: 26 Sep 2024
https://github.com/redesignscience/alphaspace2
Protein surface topographical mapping tool
jupyter-notebook protein python surface-analysis
Last synced: 02 Oct 2024
https://github.com/bayer-science-for-a-better-life/topefind-public
Finding the pitfalls of deep learning predictors of interacting residues in antibodies ðŸ¦
antibodies artificial-intelligence biology deep-learning neural-network protein
Last synced: 26 Sep 2024
https://github.com/sethaxen/mrcfile.jl
Read and write files and manipulate data in the MRC2014 format
mrc mrc-format protein structural-biology
Last synced: 01 Oct 2024
https://github.com/PDBeurope/api-webinars
Study materials for the PDBe API webinar series in September 2020.
api-rest api-webinars bioinformatics jupyter-notebooks pdb protein protein-structure python tutorial web-components webinar
Last synced: 29 Jul 2024
https://github.com/cchrysostomou/seqtables
Tools for analyzing NGS sequence data and aligned protein sequences
aligned-sequences dna ngs-analysis ngstools pandas plotly protein
Last synced: 28 Sep 2024
https://github.com/stolarczyk/BALCONY
R package: BALCONY (Better ALignment CONsensus analYsis)
alignment conservation evolutionary-biology protein protein-tunnels
Last synced: 13 Aug 2024
https://github.com/kinow/java-biostrings
Biostrings port in Java (for study)
algorithms bioinformatics dna genetics iupac java protein r text text-processing
Last synced: 01 Oct 2024
https://github.com/sarisabban/ProtVR
Visualise a Protein in Virtual Reality
pdb protein rcsb virtual-reality vr
Last synced: 29 Jul 2024
https://github.com/yaoyinying/rosetta_finder
Rosetta Commandline Python Bindings
bioinformatics bioinformatics-tool biology protein protein-structure python3
Last synced: 01 Oct 2024
