ISSN:
1089-7690
Source:
AIP Digital Archive
Topics:
Physics
,
Chemistry and Pharmacology
Notes:
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 3×3×3 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). © 2001 American Institute of Physics.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1063/1.1332809
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