Systematic analysis of added-value in simple comparative models of protein structure.
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.
Chakravarty
Suvobrata
S
Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, New York 10029, USA.
Sanchez
Roberto
R
D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D030562:Databases, Protein; D006801:Humans; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*
D011506:Proteins