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Contact Area Difference (CAD): A Robust Measure to Evaluate Accuracy of Protein Models

Summary: Contact Area Difference (CAD): A Robust Measure to
Evaluate Accuracy of Protein Models
Ruben A. Abagyan* and Maxim M. Totrov
The Skirball Institute of
Biomolecular Medicine
Biochemistry Department,
NYU Medical Centre, 540 1st
Avenue, New York, NY,
10016, USA
A simple uni®ed measure to evaluate the accuracy of three-dimensional
atomic protein models is proposed. This measure is a normalized sum of
absolute differences of residue-residue contact surface areas calculated for
a reference structure and a model. It employs more rigorous quantitative
evaluation of a contact than previously used contact measures. We argue
that the contact area difference (CAD) number is a robust single measure
to evaluate protein structure predictions in a wide range of model accu-
racies, from ab initio and threading models to models by homology, since
it reŻects both backbone topology and side-chain packing, is smooth,
continuous and threshold-free, is not sensitive to typical crystallographic
errors and ambiguities, adequately penalizes domain and/or secondary


Source: Abagyan, Ruben - School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego


Collections: Biology and Medicine