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Summary: A Predictive Method for the Evaluation of Peptide
Binding in Pocket 1 of HLA-DRB1 via Global
Minimization of Energy Interactions
I.P. Androulakis,1 N.N. Nayak,1 M.G. Ierapetritou,1 D.S. Monos,2 and C.A. Floudas1*
1Department of Chemical Engineering, Princeton University, Princeton, New Jersey
2Department of Pediatrics, University of Pennsylvania, The Children's Hospital of Philadelphia,
Philadelphia, Pennsylvania
ABSTRACT Human leukocyte antigens
(HLA) or histocompatibility molecules are gly-
coproteins that play a pivotal role in the devel-
opment of an effective immune response. An
important function of the HLA molecules is the
ability to bind and present antigen peptides to
T lymphocytes. Presently there is no compre-
hensive way of predicting and energetically
evaluating peptide binding on HLA molecules.
To quantitatively determine the binding speci-
ficity of a class II HLA molecule interacting
with peptides, a novel decomposition approach
based on deterministic global optimization is
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