Protein Fold Recognition using Residue-Based Alignments of Sequence and Secondary Structure

Protein structure prediction aims to determine the three-dimensional structure of proteins form their amino acid sequences. When a protein does not have similarity (homology) to any known fold, threading or fold recognition methods are used to predict structure. Fold recognition methods frequently employ secondary structure, solvent accessibility, and evolutionary information to enhance the accuracy and the quality ofthe predictions. In this paper, we present a residue based alignment method as an alternative to the state-of-the-art SSEA method, originally introduced by Przytycka et al. [1], and further modified by McGuffin et al. [2]. We introduce a residue-based score function, which can incorporate amino acid similarity matrices such as BLOSUM into secondary structure similarity scoring and compute joint alignments. We show that the power ofthe SSEA method comes from the length normalization instead of the element alignment technique and similar performance can be achieved using re...

• Type: Conference
• Year: 2007
• Where: ICASSP
• Authors: Zafer Aydin, Hakan Erdogan, Yucel Altunbasak
• Keywords: Amino Acid, ICASSP 2007, Secondary Structure, Secondary Structure Similarity, Signal Processing