Analyzing the simplicial decomposition of spatial protein structures

Abstract

Background: The 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. Results: 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. Conclusion: We 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. © 2006 Brahmachary et al; licensee BioMed Central Ltd.