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mdhewei/bioinfor-claw/protein-structure-alignment
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version: "1.0.0"

Protein Structure Alignment

Compare two protein structures by superimposing them via Cα atoms (Biopython Superimposer). Computes global RMSD, highlights divergent regions, and produces a dual-colour interactive 3D viewer.

Trigger examples

  • "Align the apo and holo structures of adenylate kinase"
  • "Compare 1AKE and 4AKE, what is the RMSD?"
  • "Superimpose the AlphaFold model for P00940 against the crystal structure 1TIM"
  • "How similar are the WT and mutant protein structures?"
  • "Find flexible regions between two conformations of the same protein"

Non-triggers (use a different skill)

  • "Show me the structure of a single protein" → use protein-structure-visualizer
  • "What domains does my protein have?" → use protein-structure-for-gene
  • "Align protein sequences" → use standard sequence alignment tools

Command template

bash
cd protein-structure-analysis/protein-structure-alignment
pip install biopython matplotlib numpy pandas py3Dmol requests
 
# Two PDB IDs
python scripts/protein_structure_alignment.py \
  --pdb1 <PDB_ID_1> \
  --pdb2 <PDB_ID_2> \
  --outdir results/
 
# AlphaFold predicted vs experimental
python scripts/protein_structure_alignment.py \
  --pdb1 <PDB_ID> \
  --uniprot2 <UNIPROT_ACC> \
  --outdir results/
 
# Local files
python scripts/protein_structure_alignment.py \
  --file1 wt.pdb \
  --file2 mutant.pdb \
  --outdir results/
 
# Restrict to one chain and a residue range
python scripts/protein_structure_alignment.py \
  --pdb1 1AKE --pdb2 4AKE \
  --chain1 A --chain2 A \
  --res-start 1 --res-end 180 \
  --outdir results/

All CLI arguments

ArgumentRequiredDefaultDescription
--pdb1 / --uniprot1 / --file1Yes (one of)—Structure 1 source
--pdb2 / --uniprot2 / --file2Yes (one of)—Structure 2 source
--chain1Noall chainsChain to use in structure 1
--chain2Noall chainsChain to use in structure 2
--res-startNo—First residue number to include
--res-endNo—Last residue number to include
--outdirNoresultsOutput directory
--prefixNoautoFile prefix (default: <ID1>_vs_<ID2>)

Parameter decision guide

Signal in user requestParameter to set
Two PDB IDs to compare--pdb1 <ID> --pdb2 <ID>
AlphaFold vs experimental structure--uniprot2 <ACC> (or --uniprot1)
Local PDB files--file1 wt.pdb --file2 mutant.pdb
Multi-chain structure, compare one chain--chain1 A --chain2 A
Compare only a domain / specific region--res-start 1 --res-end 200
Apo vs holo (ligand-induced conformational change)use full chain; inspect per-residue RMSD for loop regions
Homolog comparison (different residue numbering)omit --chain — let the script pair by resseq; if numbering differs badly, use --res-start/--res-end for the conserved core
"RMSD of just the kinase domain"--res-start 50 --res-end 350 --chain1 A --chain2 A

Outputs

  • <PREFIX>.alignment_summary.tsv — global RMSD, n Cα pairs, divergent residue counts
  • <PREFIX>.per_residue_rmsd.tsv — per-residue Cα distance after superimposition
  • <PREFIX>.per_residue_rmsd.png/.pdf — bar plot coloured green (<1Å) / orange (1–3Å) / red (>3Å)
  • <PREFIX>.superimposed.html — interactive 3D viewer: structure 1 in blue, structure 2 in red; divergent residues (>3Å) highlighted in orange sticks
  • <PREFIX>.superimposed.pdb — coordinates of structure 2 in the superimposed frame

How it works

  1. Fetches both structures from RCSB PDB or AlphaFold EBI (or reads local files)
  2. Extracts Cα atoms from both; pairs residues by (chain, resseq)
  3. Superimposes structure 2 onto structure 1 using Biopython's Superimposer (SVD-based rigid-body alignment)
  4. Computes global RMSD and per-residue Cα distance
  5. Writes all atoms of structure 2 in the new (rotated/translated) frame
  6. Visualises both structures in py3Dmol with divergent regions highlighted

Failure conditions

  • "No common Cα pairs found" → chains or residue numbering don't overlap; specify --chain1/--chain2 or --res-start/--res-end
  • Very high RMSD on short alignments → try aligning a specific domain with --res-start/--res-end
  • AlphaFold fetch fails → UniProt accession not found; verify at https://alphafold.ebi.ac.uk
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