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Protein Science (2006), 15:1579-1596. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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CIRSE: A solvation energy estimator compatible with flexible protein docking and design applications

David S. Cerutti1, Tushar Jain2 and J. Andrew McCammon1,2,3

1 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0365, USA
2 Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365, USA
3 Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0636, USA

(RECEIVED November 17, 2005; FINAL REVISION April 3, 2006; ACCEPTED April 7, 2006)

We present the Coordinate Internal Representation of Solvation Energy (CIRSE) for computing the solvation energy of protein configurations in terms of pairwise interactions between their atoms with analytic derivatives. Currently, CIRSE is trained to a Poisson/surface-area benchmark, but CIRSE is not meant to fit this benchmark exclusively. CIRSE predicts the overall solvation energy of protein structures from 331 NMR ensembles with 0.951 ± 0.047 correlation and predicts relative solvation energy changes between members of individual ensembles with an accuracy of 15.8 ± 9.6 kcal/mol. The energy of individual atoms in any of CIRSE's 17 types is predicted with at least 0.98 correlation. We apply the model in energy minimization, rotamer optimization, protein design, and protein docking applications. The CIRSE model shows some propensity to accumulate errors in energy minimization as well as rotamer optimization, but these errors are consistent enough that CIRSE correctly identifies the relative solvation energies of designed sequences as well as putative docked complexes. We analyze the errors accumulated by the CIRSE model during each type of simulation and suggest means of improving the model to be generally useful for all-atom simulations.

Keywords: protein docking; protein design; pair-additive; solvation; Poisson electrostatics; rotamer library; dead-end elimination


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[Abstract] [Full Text] [PDF]


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