Abstract
BackgroundThe fast growing Protein Data Bank contains the three-dimensional description of more than 45000 protein- and nucleic-acid structures today. The large majority of the data in the PDB are measured by X-ray crystallography by thousands of researchers in millions of work-hours. Unfortunately, lots of structural errors, bad labels, missing atoms, falsely identified chains and groups make dificult the automated processing of this treasury of structural biological data.ResultsAfter we performed a rigorous re-structuring of the whole PDB on graph-theoretical basis, we created the RS-PDB (Rich-Structure PDB) database. Using this cleaned and repaired database, we defined simplicial complexes on the heavy-atoms of the PDB, and analyzed the tetrahedra for geometric properties.ConclusionWe have found surprisingly characteristic differences between simplices with atomic vertices of different types, and between the atomic neighborhoods – described also by simplices – of different ligand atoms in proteins.
Highlights
The fast growing Protein Data Bank contains the three-dimensional description of more than 45000 protein- and nucleic-acid structures today
The information stored in the Protein Data Bank [1] would make possible fully automated in silico studies if mislabeled chemical groups, broken protein- and nucleic acid chains and other errors were corrected
The resulting RS-PDB database is capable to serve intricate structural queries on all the three-dimensional protein structures known to mankind
Summary
After we performed a rigorous re-structuring of the whole PDB on graph-theoretical basis, we created the RS-PDB (Rich-Structure PDB) database. Using this cleaned and repaired database, we defined simplicial complexes on the heavy-atoms of the PDB, and analyzed the tetrahedra for geometric properties
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