کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
4637667 1631978 2017 20 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Geometric and electrostatic modeling using molecular rigidity functions
ترجمه فارسی عنوان
مدلسازی هندسی و الکترواستاتیک با استفاده از توابع سفتی مولکولی
کلمات کلیدی
شاخص سختی انعطاف پذیر، عملکرد سختی سطح مولکولی، انحنای
موضوعات مرتبط
مهندسی و علوم پایه ریاضیات ریاضیات کاربردی
چکیده انگلیسی

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. The 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 proposed a rigidity based Poisson–Boltzmann equation for biomolecular electrostatic analysis. Our 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.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Computational and Applied Mathematics - Volume 313, 15 March 2017, Pages 18–37
نویسندگان
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