Sequence design in lattice models by graph theoretical methods

Sanjeev, BS and Patra, SM and Vishveshwara, S (2001) Sequence design in lattice models by graph theoretical methods. In: Journal of Chemical Physics, 114 (4). pp. 1906-14.

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Abstract

A general strategy has been developed based on graph theoretical methods, for finding amino acid sequences that take up a desired conformation as the native state. This problem of inverse design has been addressed by assigning topological indices for the monomer sites (vertices) of the polymer on a 3X3X3 cubic lattice. This is a simple design strategy, which takes into account only the topology of the target protein and identifies the best sequence for a given composition. The procedure allows the design of a good sequence for a target native state by assigning weights for the vertices on a lattice site in a given conformation. It is seen across a variety of conformations that the predicted sequences perform well both in sequence and in conformation space, in identifying the target conformation as native state for a fixed composition of amino acids. Although the method is tested in the framework of the HP model [K. F. Lau and K. A. Dill, Macromolecules 22, 3986 (1989)] it can be used in any context if proper potential functions are available, since the procedure derives unique weights for all the sites (vertices, nodes) of the polymer chain of a chosen conformation (graph).

Item Type:	Journal Article
Publication:	Journal of Chemical Physics
Publisher:	American Institute of Physics (AIP)
Additional Information:	The DOI is currently only displayed. Copyright for this article belongs to American Institute of Physics (AIP)
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	09 Jun 2004
Last Modified:	19 Sep 2010 04:12
URI:	http://eprints.iisc.ac.in/id/eprint/245

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