ISSN 1996-5362

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"" 2007-2012

 

EFFECT OF PROTEIN 3D STRUCTURE CHOICE ON THE RESULTS OF VIRTUAL SCREENING: CASPASE7 PROTEIN CASE STUDY

A.Lizunov

Applied Acoustics Research Institute; 7A, 9th May Str., Dubna City, Moscow Region, 141980, Russia; al_bio@mail.ru

This paper considers six different 3D structures of caspase7 protein from Protein Data Bank. The distance between structures is defined as RMSD between corresponding active sites' atoms of 3D structures after alignment. Despite the distances between the complexes being less than the resolution of the PDB structures, the results of virtual screening tests significantly differ for these structures. Score frequency distributions of binders and nonbinders were used for the analysis of the results of virtual screening tests. The structures split into two groups: 3 structures have nearly identical score frequency distributions for binders and nonbinders, while 3 other structures have similar distributions of binders with two peaks, which allows to distinguish part of binders from all nonbinders by score. The key feature of structures that allows to distinguish part of binders by score is the position of single residue TYR230, which turns aside and opens a buried part of caspase7 active site.

Key words: virtual screening, protein structure effect, caspase7, docking, initial data dependence.