Probability Density Profile Analysis: A Method for Identifying Novel Protein Structures

Although a number of scientific advances have been made in the area of structural biology, a few obstacles continue to impede our ability to quickly and efficiently characterize protein structure-function relationships. Probability Density Profile Analysis (PDPA) is a method which rapidly quantifies the structural novelty of a protein, based on the statistical analyses of a minimal amount of empirical data. Here we present findings related to the sensitivity and range of applicability of PDPA. Our results support the conclusion that two dimensional PDPA (2DPDPA) can reliably be utilized for identification of a protein structure to within 3Å of the known structure, using a library of existing structures. Furthermore, the sensitivity of 2D-PDPA has been tested using proteins containing different secondary structural characteristics (α, β, and α/β) and our preliminary investigations support the conclusion that 2D-PDPA is equally applicable to all general classes of proteins.