FITTING PROTEIN CHAINS TO CUBIC LATTICE IS NP-COMPLETE-Reference-Cited by-同舟云学术

FITTING PROTEIN CHAINS TO CUBIC LATTICE IS NP-COMPLETE

Published:2008-02 Issue:01 Volume:06 Page:93-106
ISSN:0219-7200
Container-title:Journal of Bioinformatics and Computational Biology
language:en
Short-container-title:J. Bioinform. Comput. Biol.

Author:

MAŇUCH JÁN¹,GAUR DAYA RAM²

Affiliation:

1. School of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada

2. Department of Math and Computer Science, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada

Abstract

It is known that folding a protein chain into a cubic lattice is an NP-complete problem. We consider a seemingly easier problem: given a three-dimensional (3D) fold of a protein chain (coordinates of its C α atoms), we want to find the closest lattice approximation of this fold. This problem has been studied under names such as "lattice approximation of a protein chain", "the protein chain fitting problem", and "building of protein lattice models". We show that this problem is NP-complete for the cubic lattice with side close to 3.8 Å and coordinate root mean square deviation.

Publisher

World Scientific Pub Co Pte Lt

Subject

Computer Science Applications,Molecular Biology,Biochemistry

Link

https://www.worldscientific.com/doi/pdf/10.1142/S0219720008003308

Reference18 articles.

1. Theory for the folding and stability of globular proteins

2. Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete

3. Exploring conformational space with a simple lattice model for protein structure

4. Principles of protein folding - A perspective from simple exact models

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