protein-structure-analysis

To calculate RMSD, the skill parses PDB or mmCIF files, filters for C-alpha atoms, and applies superposition logic to align the structures. This prevents common geometry errors during structural comparison.

PDB to PDBQT format conversion for molecular docking is handled through pipeline integration features. The skill automates this conversion process, ensuring proper formatting for docking software compatibility and reproducible results.

Binding pocket detection is automated using fpocket integration. The skill standardizes this structural biology workflow by identifying potential binding sites through geometric calculations, eliminating manual errors in pocket detection tasks.

Yes, Ramachandran plot generation and contact map analysis are supported as core structural analysis features. The skill automates these tasks alongside DSSP secondary structure assignment for comprehensive evaluation.

Yes, Biopython, PyMOL, and fpocket are required dependencies to execute geometric calculations and structural alignments accurately. They must be installed to support PDB parsing, pocket detection, and superposition tasks.

Binding site flexibility comparison across NMR models often fails due to incorrect atom filtering and superposition logic. The skill standardizes these geometric calculations to prevent common alignment errors in multi-model analysis.