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BMC Bioinformatics. 2008;9 Suppl 1:S11. doi: 10.1186/1471-2105-9-S1-S11.

Analyzing the simplicial decomposition of spatial protein structures.

Author information

1
Protein Information Technology Group, Department of Computer Science, Eötvös University, Pázmány P, stny., 1/C, H-1117 Budapest, Hungary. devill@cs.elte.hu

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.

PMID:
18315842
PMCID:
PMC2259412
DOI:
10.1186/1471-2105-9-S1-S11
[Indexed for MEDLINE]
Free PMC Article

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