Analyzing the simplicial decomposition of spatial protein structures.
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.


CONCLUSIONS
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.
Ordög
Rafael
R
Protein Information Technology Group, Department of Computer Science, Eötvös University, Pázmány P, stny., 1/C, H-1117 Budapest, Hungary. devill@cs.elte.hu
Szabadka
Zoltán
Z
Grolmusz
Vince
V
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D020539:Sequence Analysis, Protein / Q000379:methods*
D011506:Proteins