title: Cysteine and tryptophan anomalies found when scanning all the binding sites in the Protein Data Bank.
abstract: The Protein Data Bank (PDB) is one of the richest sources of structural biological information in the World. It started to exist as the computer-readable depository of crystallographic data complementing printed papers. The proper interpretation of the content of the individual files in the PDB still needs the detailed information found in the citing publication. An advanced graph theoretical method is presented here for automatically repairing, re-organising and re-structuring PDB data yielding the identification of all the protein-ligand complexes and all the binding sites in the PDB. As an application, we identified strong cysteine and tryptophan irregularities in the data.
authors.affiliation: Protein Information Technology Group, Eotvos University, H-1117 Budapest, Hungary. hugeaux@cs.elte.hu
authors.forename: Gábor
authors.initials: G
authors.lastname: Iván
authors.forename: Zoltán
authors.initials: Z
authors.lastname: Szabadka
authors.forename: Vince
authors.initials: V
authors.lastname: Grolmusz
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D003545:Cysteine / Q000737:chemistry* / Q000235:genetics; D030562:Databases, Protein; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D014364:Tryptophan / Q000737:chemistry* / Q000235:genetics
chemical_list: D011506:Proteins; D014364:Tryptophan; D003545:Cysteine