Structure Contact Analysis

Identify peptide–protein contact hotspots from a PDB structure (local file or fetched from RCSB) and emit binding hotspot positions.

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Structure Contact Analysis

Given a PDB ID (or a local PDB file), compute residue-level contacts between a short peptide chain and a protein chain.

Outputs include:

  • inferred peptide chain + sequence
  • contact counts per peptide residue
  • top hotspot positions suitable for protecting during mutation generation

CLI

python3 scripts/run.py --pdb-id 7T10
python3 scripts/run.py --query "SSTR2 octreotide receptor"
python3 scripts/run.py --pdb-path tests/fixtures/mini_complex.pdb

lamm-mit/scienceclaw/tree/main/skills/structure-contact-analysis commit 489e482cfa

Frequently asked questions

npx skillmds@latest add lamm-mit/structure-contact-analysis