title: Searching protein 3-D structures for optimal structure alignment using intelligent algorithms and data structures.
abstract: In this paper, we present a novel algorithm for measuring protein similarity based on their 3-D structure (protein tertiary structure). The algorithm used a suffix tree for discovering common parts of main chains of all proteins appearing in the current research collaboratory for structural bioinformatics protein data bank (PDB). By identifying these common parts, we build a vector model and use some classical information retrieval (IR) algorithms based on the vector model to measure the similarity between proteins--all to all protein similarity. For the calculation of protein similarity, we use term frequency × inverse document frequency ( tf × idf ) term weighing schema and cosine similarity measure. The goal of this paper is to introduce new protein similarity metric based on suffix trees and IR methods. Whole current PDB database was used to demonstrate very good time complexity of the algorithm as well as high precision. We have chosen the structural classification of proteins (SCOP) database for verification of the precision of our algorithm because it is maintained primarily by humans. The next success of this paper would be the ability to determine SCOP categories of proteins not included in the latest version of the SCOP database (v. 1.75) with nearly 100% precision.
authors.affiliation: Department of Computer Science, Vysoká Skola Báňská—Technical University of Ostrava, Ostrava 70833, Czech Republic. tomas.novosad@vsb.cz
authors.forename: Tomáš
authors.initials: T
authors.lastname: Novosád
authors.forename: Václav
authors.initials: V
authors.lastname: Snášel
authors.forename: Ajith
authors.initials: A
authors.lastname: Abraham
authors.forename: Jack Y
authors.initials: JY
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins