alterlab-pdb
From the author
Access the RCSB Protein Data Bank (PDB) for EXPERIMENTALLY determined 3D structures (X-ray, cryo-EM, NMR) of proteins and nucleic acids — searching by text, sequence, or structure similarity and downloading coordinates in PDB/mmCIF format with metadata. Use when retrieving a structure by PDB ID, running sequence or structure similarity searches, or obtaining experimental coordinates for structural biology and drug discovery; for AI-PREDICTED structures of proteins lacking experimental data prefer alterlab-alphafold-db, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.
Install
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-pdb -a claude-code
Installs to .claude/skills/alterlab-pdb/ · Each command fetches the skill straight from GitHub with the open skills CLI.
Byte-identical to the scanned commit, with the repository’s licence and a SOURCE.txt.
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Similar skills
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- alterlab-uniprotAlterLab-IEU/AlterLab-Academic-SkillsProvide direct REST API access to UniProt (Swiss-Prot/TrEMBL) for protein sequence searches, FASTA retrieval, functional annotations (GO terms, domains), and cross-database ID mapping. Use when looking up a protein entry, fetching a protein FASTA sequence, or mapping accessions between databases over raw HTTP/REST; for EXPERIMENTAL 3D structures prefer alterlab-pdb, for AI-PREDICTED 3D structures prefer alterlab-alphafold-db, for protein-protein interaction networks prefer alterlab-string-db, and for Python workflows spanning many databases prefer alterlab-bioservices instead. Part of the AlterLab Academic Skills suite.Data★ 78
- pdb-databasejaechang-hits/SciAgent-SkillsQuery RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, attribute, sequence, or 3D structure similarity (Search API); retrieve metadata via GraphQL (Data API); download PDB/mmCIF from files.rcsb.org. For AlphaFold predictions use alphafold-database-access; for protein sequences only use uniprot-protein-database.Data★ 383
- pdbBioTender-max/awesome-bio-agent-skillsFetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific chains or domains, (5) Get structure metadata. For sequence lookup, use uniprot. For binder design workflow, use binder-design.Design★ 206
- alterlab-interproAlterLab-IEU/AlterLab-Academic-SkillsQuery the EMBL-EBI InterPro REST API for protein family, domain, and functional-site annotations integrated from member databases (Pfam, PANTHER, PRINTS, SMART, SUPERFAMILY, CDD, ProSite, NCBIfam, and others). Use when predicting protein function, analyzing or comparing domain architecture, classifying a protein by family or homologous superfamily, resolving a Pfam/InterPro accession, or mapping a protein's signatures to GO terms. Not for raw UniProt entry/FASTA retrieval or AlphaFold 3D structures. Part of the AlterLab Academic Skills suite.Science★ 78
- alterlab-string-dbAlterLab-IEU/AlterLab-Academic-SkillsQuery the STRING API for protein-protein interactions (59M proteins, 20B+ interactions across 12,500+ organisms), building interaction networks, discovering functional partners, and running GO/KEGG/Pfam enrichment on protein lists. Use when constructing a protein-protein interaction network, expanding from seed proteins to functional partners, or running PPI-based enrichment for systems biology; for curated metabolic pathway maps and reactions prefer alterlab-kegg, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.Science★ 78
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