Title

Systematic Analysis of Added-Value in Simple Comparative Models of Protein Structure

Document Type

Article

Publication Date

8-2004

Abstract

Added-value is the additional information that a model carries with respect to the template structure used for model building. Thousands of single-template models, corresponding to proteins of known structure, were analyzed. The accuracy of structure-derived properties, such as residue accessibility, surface area, electrostatic potential, and others, was determined as a function of template:target sequence identity by comparing the models with their corresponding experimental structures. Added-value was determined by comparing the accuracy in models with that from templates. Geometry-dependent properties such as neighborhood of buried residues and accessible surface area showed low added-value. Properties that also depend on the protein sequence, such as presence of polar areas and electrostatic potential, showed high added-value. In general added-value increases when template:target sequence identity decreases, but it is also affected by alignment errors. This study justifies the use of models instead of the use of templates to estimate structure-derived properties of a target protein.

Publication Title

Structure

Volume

12

Issue

8

First Page

1461

Last Page

1470

DOI of Published Version

10.1016/j.str.2004.05.018

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