STON: A novel method for protein three-dimensional structure comparison

  • Authors:

  • Changiz Eslahchi;Hamid Pezeshk;Mehdi Sadeghi;Amir Massoud Rahimi;Heydar Maboudi Afkham;Shahriar Arab

  • Affiliations:

  • Department of Mathematical Sciences, Shahid Beheshti University, Post Code 1983963113, Tehran, Iran and School of Computer Science, Institute for Research in Fundamental Sciences(IPM), P.O. Box 19 ...;School of Mathematics, Statistics and Computer Science and Center of Excellence in Biomathematics, University College of Science, University of Tehran, P.O. Box 14155-6455, Tehran, Iran;National Institute of Genetic Engineering and Biotechnology, P.O. Box 14155-6343, Tehran, Iran;School of Computer Science, Institute for Research in Fundamental Sciences(IPM), P.O. Box 19395-5746, Tehran, Iran;Department of Mathematical Sciences, Shahid Beheshti University, Post Code 1983963113, Tehran, Iran;Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, P.O. Box 13145-1384, Tehran, Iran

  • Venue:
  • Computers in Biology and Medicine
  • Year:
  • 2009

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Abstract

Protein structure comparison is an important problem in bioinformatics and has many applications in the study of structural and functional genomics. During the last decades, various heuristic methods have been developed to solve the protein structure comparison problem. Most of the protein structure comparison methods give the alignment based on the minimum RMSD (root mean square deviation) and ignore many significant local alignments that may be important for evolutional or functional studies. We have developed a new algorithm to find aligned residues in two proteins with desired RMSD value. The parameterized distance and rotation in this program enable us to search for strongly or weakly similar aligned fragments in two proteins.