Identify residue contacts shared across all or most protein structures of a give protein family
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Sep 22, 2019 - Python
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protein-structures
Here are 16 public repositories matching this topic...
Diffusion Kernel-based Graph Node Clustering for Protein Domain Assignment
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Sep 13, 2022 - Python
Find all PDB structures associated with a UniProt entry. #Haku
python bioinformatics structural-biology jupyter-notebook protein-sequences uniprot protein-structures
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Aug 22, 2025 - Jupyter Notebook
ProteinInteractionFinder (PIF) is a Java 11 library for determining interatomic interactions in protein structures, obtained from PDB (Protein Data Bank) files.
pdb pif identification protein-structures interatomic-interactions intraprotein-interactions protein-interaction-finder
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Jun 17, 2021 - Java
Yale Gradute School module CBB752 final group project by Jiaqi Li, Keyi Li, and Anna Su.
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Apr 26, 2023 - Jupyter Notebook
python bioinformatics structural-biology pdb scientific-computing data-analysis jupyter-notebooks pdbe protein-structures
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Aug 27, 2026 - Jupyter Notebook
List the protein chains and ligands in structural file(s). #Haku
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Mar 3, 2026 - Python
Archived research prototype for immunogenic peptide design and docking.
python bioinformatics molecular-docking protein-structures alphafold2 immunogenic-peptides autodockvina peptide-design
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May 17, 2023 - Jupyter Notebook
The official repository of the Nexus Resonance Codex (NRC)
math protein-structure mathematics artificial-intelligence artificial-neural-networks protein-sequences number-theory artificial-intelligence-algorithms protein-folding millennium-problems protein-structure-prediction protein-structure-analysis protein-structures folding-at-home protein-structure-alignment protein-folding-prediction ai-enhancements erdos-problems
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Sep 27, 2026 - Python
BioStructures Image Database and Experiments Schema
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Oct 29, 2025 - Python
Clusters protein chains based on CA distance difference
python bioinformatics structural-biology computational-biology structural-analysis protein-clustering distance-matrix protein-structures protein-conformation
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Oct 9, 2026 - Python
PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.
python bioinformatics structural-biology mcp api-server knowledge-graph pdbe protein-structures llm-tools ai-integration
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Oct 27, 2026 - Python
Next-generation protein-protein interaction site (PPIS) prediction integrating ESM-2 protein language model representations with structural & evolutionary features via biophysics-supervised gated fusion and equivariant graph networks.
bioinformatics deep-learning pytorch protein-protein-interaction graph-neural-networks protein-structures graph-transformer egnn esm2 ppis-prediction
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Oct 8, 2026 - Python
Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.
python scraper bioinformatics database genomics genbank protein-sequences carbohydrates enzymes protein-structures gtdb cazy cazymes cazy-family cazy-webscraper
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Aug 31, 2026 - Python
PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
bioinformatics pymol-plugin pymol protein-sequences sequence-alignments homology-modeling protein-structures structural-alignments similarity-searches
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Jul 10, 2026 - Python
A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.
tomography electron-microscopy cryo-em 3d-reconstruction density-map model-building cryoem protein-structures 3d-denoise
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Jan 25, 2021
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