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J Comput Chem. 2014 Apr 5;35(9):737-47. doi: 10.1002/jcc.23547. Epub 2014 Feb 5.

Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis.

Author information

  • 1State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China.

Abstract

The reliability of the linear interaction energy (LIE) depends on the atomic charge model used to delineate the Coulomb interaction between the ligand and its environment. In this work, the polarized protein-specific charge (PPC) implementing a recently proposed fitting scheme has been examined in the LIE calculations of the binding affinities for avidin and β-secretase binding complexes. This charge fitting scheme, termed delta restrained electrostatic potential, bypasses the prevalent numerical difficulty of rank deficiency in electrostatic-potential-based charge fitting methods via a dual-step fitting strategy. A remarkable consistency between the predicted binding affinities and the experimental measurement has been observed. This work serves as a direct evidence of PPC's applicability in rational drug design.

KEYWORDS:

avidin; charge model; force field; linear interaction energy; polarization; β-secretase

PMID:
24500844
DOI:
10.1002/jcc.23547
[PubMed - indexed for MEDLINE]
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