pdb2site

usage: pdb2site [options] pdbfile sitefile ligandfile

pdb2site is a rule-based program that extracts the macromolecule and bound ligand(s) from a PDB file. Waters which may be important for ligand binding are selected ("+/-waters") based on their LIGSITE (burial) score ("-water_score") and the number of contacts they make with the macromolecule and the ligand ("-water_contacts"). Metals and hydrogens may be selected or rejected through command-line options "+/-metals" and "+/-hydrogens".

pdb2site recognizes common cofactors and coenzymes (FS4, HEM, COA, FAD, NAD, NAP, NDP) plus standard amino acid and nucleic acid residues as part of the macromolecule. Residues ASX, CYH, CSH, CSM, CPR, EXC, FOR, GLX, HYD, HYP, PCA, and UNK are also assigned as macromolecule. Waters are recognized by residue names HOH, H20, TIP, WAT, DOD, and D2O. Other solvents or counterions are recognized by residue names ACY, DMS, SO4, SOL, SEO, SUL, and PO4.

Atoms from disordered segments are recognized and arbitrarily selected to ensure that only one copy of each residue and atom is present in the final structure.

If multiple candidate ligands are found, the largest connected fragment is selected. If no candidate ligands are found, the smallest connected fragment from the macromolecule is selected (e.g. a bound peptide).

Multimeric proteins are frequently deposited in the PDB in a non-relevant form for ligand binding; e.g. a tetrameric protein might be deposited as a monomer, or a monomeric protein as a tetramer! pdb2site does NOT recognize or even attempt to solve this problem. The correct multimeric form for many proteins can be found at the Protein Quaternary Structure (PQS) server and downloaded.

Reference

LIGSITE: M. Hendlich, F. Rippmann, and G. Barnickel, J. Mol. Graphics, 15, 359-363 (1997).