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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.

SUBMITTER: Ordog R

PROVIDER: S-EPMC2259412 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Analyzing the simplicial decomposition of spatial protein structures.

Ordög Rafael R Szabadka Zoltán Z Grolmusz Vince V

BMC bioinformatics 20080101

<h4>Background</h4>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.<h4>Results</ ...[more]

PMID: 18315842

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