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Summary: Homology Modeling With Internal Coordinate
Mechanics: Deformation Zone Mapping and
Improvements of Models via Conformational Search
Ruben Abagyan,* Serge Batalov, Timothy Cardozo, Maxim Totrov, Jeremy Webber, and Yingyao Zhou
Skirball Institute of Biomolecular Medicine, Biochemistry Department, New York University Medical Center,
New York, New York
ABSTRACT Five models by homology con-
taining insertions and deletions and ranging
from 33% to 48% sequence identity to the known
homologue, and one high sequence identity
(85%) model were built for the CASP2 meeting.
For all five low identity targets: (i) our starting
models were improved by the Internal Coordi-
nate Mechanics (ICM) energy optimization, (ii)
the refined models were consistently better
than those built with the automatic SWISS-
MODEL program, and (iii) the refined models
differed by less than 2% from the best model
submitted, as judged by the residue contact
area difference (CAD) measure [Abagyan, R.A.,
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