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On a characterization of the folding of proteins

✍ Scribed by Milan Randić; Goran Krilov

Publisher
John Wiley and Sons
Year
1999
Tongue
English
Weight
173 KB
Volume
75
Category
Article
ISSN
0020-7608

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✦ Synopsis

We consider a characterization of the folding of 3-D model proteins.

Using as the input the geometry of molecules, we first construct a distancerdistance matrix in which element i, j is given by the quotient of the Euclidean and the graph theoretical distance between the two vertices. The leading eigenvalue of the DrD matrix gives a measure of the folding of the protein structure. Using higher powers of the Ž . elements of DrD matrices, we generate the corresponding leading eigenvalue k for Ž . different exponents k s 1, 2, 3, . . . . So, derived invariants represent a characterization of the folding of a structure-here, model proteins. The derived invariants are analogous to the characterization of proteins based on the average distance, referred to as a protein profile. The folding index s rn, that is, the leading eigenvalue, is normalized to the number of ''points'' representing the structure. Structures that are more folded have a smaller folding index. We illustrate the use of the folding indices to measure the degree of similarity of molecules.

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