Geometric and electrostatic modeling using molecular rigidity functions

Mu, Lin; Xia, Kelin; Wei, Guowei

doi:10.1016/j.cam.2016.08.019

Title: Geometric and electrostatic modeling using molecular rigidity functions

Journal Article · Wed Mar 01 00:00:00 EST 2017 · Journal of Computational and Applied Mathematics

DOI:https://doi.org/10.1016/j.cam.2016.08.019· OSTI ID:1771195

; Xia, Kelin; Wei, Guowei

Geometric and electrostatic modeling is an essential component in computational biophysics and molecular biology. Commonly used geometric representations admit geometric singularities such as cusps, tips and self-intersecting facets that lead to computational instabilities in the molecular modeling. Our present work explores the use of flexibility and rigidity index (FRI), which has a proved superiority in protein B-factor prediction, for biomolecular geometric representation and associated electrostatic analysis. FRI rigidity surfaces are free of geometric singularities. We propose a rigidity based Poisson–Boltzmann equation for biomolecular electrostatic analysis. These approaches to surface and electrostatic modeling are validated by a set of 21 proteins. Our results are compared with those of established methods. Finally, being smooth and analytically differentiable, FRI rigidity functions offer excellent curvature analysis, which characterizes concave and convex regions on protein surfaces. Polarized curvatures constructed by using the product of minimum curvature and electrostatic potential is shown to predict potential protein–ligand binding sites.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1771195

Alternate ID(s):: OSTI ID: 1329763; OSTI ID: 1358866

Journal Information:: Journal of Computational and Applied Mathematics, Journal Name: Journal of Computational and Applied Mathematics Vol. 313 Journal Issue: C; ISSN 0377-0427

Publisher:: ElsevierCopyright Statement

Country of Publication:: Belgium

Language:: English

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Cited by: 6 works

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Title: Geometric and electrostatic modeling using molecular rigidity functions

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