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Literature DB >> 17912422

The Gaussian Generalized Born model: application to small molecules.

J A Grant¹, B T Pickup, M J Sykes, C A Kitchen, A Nicholls.

Abstract

This work presents a Generalized Born model for the computation of the electrostatic component of solvation energies which is based on volume integration. An analytic masking function is introduced to remove Coulombic singularities. This approach leads to analytic formulae for the computation of Born radii, which are differentiable to arbitrary order, and computationally straightforward to implement.

Year: 2007 PMID： 17912422 DOI： 10.1039/b707574j

Source DB: PubMed Journal: Phys Chem Chem Phys ISSN： 1463-9076 Impact factor: 3.676

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Cited

21 in total

1. Differential geometry based solvation model II: Lagrangian formulation.

Authors: Zhan Chen; Nathan A Baker; G W Wei
Journal: J Math Biol Date: 2011-01-30 Impact factor: 2.259

2. Parameter optimization in differential geometry based solvation models.

Authors: Bao Wang; G W Wei
Journal: J Chem Phys Date: 2015-10-07 Impact factor: 3.488

3. An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions.

Authors: Ramu Anandakrishnan; Alexey V Onufriev
Journal: J Comput Chem Date: 2010-03 Impact factor: 3.376

Review 4. Biomolecular electrostatics and solvation: a computational perspective.

Authors: Pengyu Ren; Jaehun Chun; Dennis G Thomas; Michael J Schnieders; Marcelo Marucho; Jiajing Zhang; Nathan A Baker
Journal: Q Rev Biophys Date: 2012-11 Impact factor: 5.318

5. On the Dielectric Boundary in Poisson-Boltzmann Calculations.

Authors: Harianto Tjong; Huan-Xiang Zhou
Journal: J Chem Theory Comput Date: 2008-02-21 Impact factor: 6.006

6. Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber.

Authors: Saeed Izadi; Ramu Anandakrishnan; Alexey V Onufriev
Journal: J Chem Theory Comput Date: 2016-11-07 Impact factor: 6.006

The Gaussian Generalized Born model: application to small molecules.

1. Differential geometry based solvation model II: Lagrangian formulation.

2. Parameter optimization in differential geometry based solvation models.

3. An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions.

Review 4. Biomolecular electrostatics and solvation: a computational perspective.

5. On the Dielectric Boundary in Poisson-Boltzmann Calculations.

6. Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber.

Review 7. Generalized Born Implicit Solvent Models for Biomolecules.

8. Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations.

Review 9. Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins.

10. Assessing the performance of implicit solvation models at a nucleic acid surface.