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A normalized root-mean-square distance for comparing protein three-dimensional structures.

ABSTRACT: The degree of similarity of two protein three-dimensional structures is usually measured with the root-mean-square distance between equivalent atom pairs. Such a similarity measure depends on the dimension of the proteins, that is, on the number of equivalent atom pairs. The present communication presents a simple procedure to make the root-mean-square distances between pairs of three-dimensional structures independent of their dimensions. This normalization may be useful in evolutionary and fold classification studies as well as in simple comparisons between different structural models.

SUBMITTER: Carugo O

PROVIDER: S-EPMC2374114 | biostudies-literature | 2001 Jul

REPOSITORIES: biostudies-literature

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A normalized root-mean-square distance for comparing protein three-dimensional structures.

Carugo O O Pongor S S

Protein science : a publication of the Protein Society 20010701 7

The degree of similarity of two protein three-dimensional structures is usually measured with the root-mean-square distance between equivalent atom pairs. Such a similarity measure depends on the dimension of the proteins, that is, on the number of equivalent atom pairs. The present communication presents a simple procedure to make the root-mean-square distances between pairs of three-dimensional structures independent of their dimensions. This normalization may be useful in evolutionary and fol ...[more]

PMID: 11420449

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