---
name: protein-structure-38806ec61d2e
description: Analyzes protein 3D structures, performs homology modeling, interprets AlphaFold predictions, conducts molecular docking, and evaluates protein-ligand interactions; trigger when users ask about PDB files, folding, binding sites, or structural biology.
---

## When to Trigger

Activate this skill when the user mentions:
- Protein folding, AlphaFold, ESMFold, RoseTTAFold
- PDB files, structural analysis, Ramachandran plots
- Molecular docking, binding affinity, binding pockets
- Homology modeling, threading, ab initio structure prediction
- Protein-protein interactions (PPI), interface analysis
- Structural alignment, RMSD, TM-score
- Cryo-EM, X-ray crystallography data interpretation

## Step-by-Step Methodology

1. **Retrieve or predict structure** - Search PDB for experimental structures (by UniProt ID or gene name). If unavailable, use AlphaFold DB or run ESMFold. Check pLDDT confidence scores for predicted structures.
2. **Quality assessment** - For experimental structures: check resolution, R-free, and completeness. For predictions: evaluate pLDDT per-residue and PAE (predicted aligned error) matrices.
3. **Structural analysis** - Identify secondary structure elements (helices, sheets, loops). Compute solvent-accessible surface area. Map conserved residues and functional domains.
4. **Binding site identification** - Use fpocket, SiteMap, or DoGSiteScorer for pocket detection. Cross-reference with known ligand binding from PDBe or BindingDB.
5. **Molecular docking** - Recommend AutoDock Vina, GNINA, or Glide. Define grid box around binding site. Report binding energy (kcal/mol) and key interactions (H-bonds, hydrophobic, pi-stacking).
6. **Structural comparison** - Align structures using TM-align or FATCAT. Report RMSD and TM-score. Identify conformational changes between states.
7. **Visualization guidance** - Recommend PyMOL, ChimeraX, or Mol* for rendering. Specify coloring schemes (by chain, B-factor, electrostatics, or conservation).

## Key Databases and Tools

- **PDB / PDBe** - Experimental protein structures
- **AlphaFold DB** - AI-predicted structures for UniProt entries
- **UniProt** - Protein sequences, domains, and annotations
- **InterPro / Pfam** - Domain classification
- **BindingDB / ChEMBL** - Binding affinity data
- **RCSB PDB REST API** - Programmatic structure queries
- **PDBe-KB** - Aggregated structural annotations

## Output Format

- Report structures with PDB ID, resolution, method, and chain identifiers.
- Binding energies in kcal/mol with interaction fingerprints.
- Structural alignments with RMSD (in Angstroms) and TM-score.
- Residue numbering must match the canonical UniProt sequence or PDB SEQRES.
- Include PyMOL/ChimeraX commands for reproducing visualizations.

## Quality Checklist

- [ ] Structure source and method (X-ray, cryo-EM, NMR, predicted) clearly stated
- [ ] Resolution or confidence metric (pLDDT) reported
- [ ] Binding site residues listed with chain and numbering
- [ ] Docking results include top poses and interaction details
- [ ] Limitations of predicted structures acknowledged where relevant
- [ ] All PDB IDs verified as valid and current
- [ ] Biological assembly vs. asymmetric unit distinguished


---
Source attribution: beita6969
Original project: https://github.com/beita6969/ScienceClaw/blob/e925f732c7ca435f557e88075bc47a58f1e984f1/skills/protein-structure/SKILL.md
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Copyright (c) 2025 Peter Steinberger

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: beita6969
Original project: https://github.com/beita6969/ScienceClaw/blob/e925f732c7ca435f557e88075bc47a58f1e984f1/skills/protein-structure/SKILL.md
Attribution basis: Source repository record

Fields of work: Data & Analytics, Education & Research
Roles: Data Scientist, Researcher
Specialties: Specialty not specified
Tools: Alphafold, Bindingdb, Chimerax, Pdbe, Pymol, Autodock Vina
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: 82e88ed31a396101a5476105ea24c25370611921665eefc3f3b04561317faa28