The inverse protein folding problem on 2D and 3D lattices

Authors:
Piotr Berman;Bhaskar DasGupta;Dhruv Mubayi;Robert Sloan;György Turán;Yi Zhang
Affiliations:
Department of Computer Science & Engineering, Pennsylvania State University, University Park, PA 16802, USA;Department of Computer Science, University of Illinois at Chicago, Chicago, IL 60607-7053, USA;Department of Mathematics, Statistics & Computer Science, University of Illinois at Chicago, Chicago, IL 60607-7045, USA;Department of Computer Science, University of Illinois at Chicago, Chicago, IL 60607-7053, USA;Department of Mathematics, Statistics & Computer Science, University of Illinois at Chicago, Chicago, IL 60607-7045, USA;Department of Computer Science, University of Illinois at Chicago, Chicago, IL 60607-7053, USA
Venue:
Discrete Applied Mathematics
Year:
2007

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Abstract

In this paper we investigate the inverse protein folding (IPF) problem under the Canonical model on 3D and 2D lattices [W.E. Hart, On the computational complexity of sequence design problems, Proceedings of the First Annual International Conference on Computational Molecular Biology 1997, pp. 128-136; E.I. Shakhnovich, A.M. Gutin, Engineering of stable and fast-folding sequences of model proteins, Proc. Natl. Acad. Sci. 90 (1993) 7195-7199]. In this problem, we are given a contact graph G=(V,E) of a protein sequence that is embeddable in a 3D (respectively, 2D) lattice and an integer 1=