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Published May 2005 | Supplemental Material
Journal Article Open

One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations


Successfully modeling electrostatic interactions is one of the key factors required for the computational design of proteins with desired physical, chemical, and biological properties. In this paper, we present formulations of the finite difference Poisson-Boltzmann (FDPB) model that are pairwise decomposable by side chain. These methods use reduced representations of the protein structure based on the backbone and one or two side chains in order to approximate the dielectric environment in and around the protein. For the desolvation of polar side chains, the two-body model has a 0.64 kcal/mol RMSD compared to FDPB calculations performed using the full representation of the protein structure. Screened Coulombic interaction energies between side chains are approximated with an RMSD of 0.13 kcal/mol. The methods presented here are compatible with the computational demands of protein design calculations and produce energies that are very similar to the results of traditional FDPB calculations.

Additional Information

© 2005 The Protein Society. Received November 29, 2004; Final revision January 19, 2005; Accepted January 20, 2005. Article first published online: 1 Jan. 2009. We thank Barry Honig and Emil Alexov for helpful conversations. This work was supported by the Howard Hughes Medical Institute, the Ralph M. Parsons Foundation, an IBM Shared University Research Grant, DARPA, ARO/ICB (S.L.M.), an NSF graduate research fellowship (C.L.V.), an NIH training grant, and the Caltech Initiative in Computational Molecular Biology program, awarded by the Burroughs Wellcome Fund (S.A.M.).

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