Fetch and analyze protein structures from RCSB PDB files.
npx skills add https://github.com/junior1p/ProteinClaw --skill pdb-junior1p
Please help me install this Agent Skill. Skill: pdb Source: https://github.com/junior1p/ProteinClaw/tree/main/skills/pdb Command: npx skills add https://github.com/junior1p/ProteinClaw --skill pdb-junior1p
Rapidly retrieve and prepare experimentally determined protein structures for downstream design and analysis workflows, removing the manual steps of downloading, trimming, and extracting chain-specific data.
Use the pdb skill to download PDB ID 1ALU, extract chain A, remove waters and ligands, and return a cleaned mmCIF file ready for design.
High-intent search queries and answers about installing and using this skill.
To extract a specific chain from a PDB file, you can fetch the structure by its ID and isolate the target chain. This process removes unwanted waters and ligands, producing a cleaned mmCIF file ready for analysis.
Preparing a protein structure for binder design involves fetching the target from RCSB, trimming unwanted components like waters, and identifying interface residues. This yields a cleaned structure directly usable by downstream design tools.
Yes, you can query the RCSB search API to find similar protein structures. By running text queries against the database, you can discover and retrieve relevant experimental structures for your analysis.
The best way to retrieve mmCIF files and FASTA sequences is to use direct HTTP access to RCSB file endpoints. This allows automated downloads of experimentally determined protein structures and their corresponding metadata.
Yes, this approach works for identifying interface residues in protein structures. It performs simple structure trimming and interface residue detection, enabling you to isolate the specific interaction surfaces needed for analysis.
You need to remove waters and ligands to prepare clean target structures for downstream design tools. This structure preparation step ensures that only the relevant protein chain and domains are processed during analysis.
qinyan-aiSearch and retrieve 3D structural data from the RCSB PDB.
junior1pRank protein binder designs using ipSAE_min, LIS, and pDockQ scores.
junior1pDesign protein sequences for given backbone structures using ProteinMPNN.
adaptyvbioFetch protein structures from the RCSB PDB API and load them for analysis.
