Examining protein folding process simulation and searching for common structure motifs in a protein family as experiments in the GridSpace2 virtual laboratory

Abstract

This paper presents two in-silico experiments from the field of bioinformatics. The first experiment covers the popular problem of protein folding process simulation and investigates the correctness of the "Fuzzy Oil Drop" model (FOD) [3], on over 60 thousands of proteins deposited in Protein Data Bank [18]. The FOD model assumes the hydrophobicity distribution in proteins to be accordant with the 3D Gauss function differentiating the hydrophobicity density from the highest in the center of the molecule, to zero level on the surface. The second experiment focuses on performing comparison of proteins that belong to the same family. Examination of proteins alignment at three different levels of protein description may lead to identifying a conservative area in protein family, which is responsible for the protein function. It also creates a possibility of determining a ligand binding site for protein, which is a key issue in drug design. Both experiments were realized as virtual experiments in the GridSpace2 Virtual Laboratory [13] Experiment Workbench [16] and were executed on Zeus cluster provided by PL-Grid. © 2012 Springer-Verlag Berlin Heidelberg.