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Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors

Evan J. Arthur, Charles L. Brooks
2016 Journal of Computational Chemistry  
The Generalized Born model with a Simple sWitching function (GBSW) addresses these issues by using an efficient approximation of Poisson-Boltzmann (PB) theory to calculate each solute atom's free energy  ...  We find that much of the algorithm scales linearly with an increase of system size, which makes this water model cost effective for solvating large systems.  ...  Josh Buckner for their assistance in CHARMM and OpenMM programming advice. This work was funded by the National Institutes of Health through grant GM103695 to CLB. Bibliography  ... 
doi:10.1002/jcc.24280 pmid:26786647 pmcid:PMC4801733 fatcat:ngj3p632kbgzzbynoxnvgrddvm

Fast Surface Based Electrostatics for biomolecules modeling [article]

P. O. Fedichev, G. N. Getmantsev, L. I. Menshikov
2009 arXiv   pre-print
We analyze deficiencies of commonly used Coulomb approximations in Generalized Born solvation energy calculation models and report a development of a new fast surface-based method (FSBE) for numerical  ...  at the surface of the molecule, both the solvation energy value and its derivatives suitable for Molecular Dynamics (MD) simulations.  ...  The solvation energy contribution method introduced this report is implemented in various models employed in Quantum Pharmaceuticals drug discovery applications. PCT application is led.  ... 
arXiv:0908.0634v2 fatcat:wwxjmuiyh5b5na7u5wpzttbm54

Dielectric response of concentrated NaCl aqueous solutions: Molecular dynamics simulations

Alexander Yu. Zasetsky, Igor M. Svishchev
2001 Journal of Chemical Physics  
radii used in generalized Born ͑GB͒ methods.  ...  , such as biological membranes or organic solvent, compared to previous methods where the calculation of Born radii does not depend on the environment.  ...  This new approach extends GB-type methods to implicit modeling of low-dielectric environments.  ... 
doi:10.1063/1.1381055 fatcat:4oymx6zwunhtrmn3jwdplmvsru

Introducing Charge Hydration Asymmetry into the Generalized Born Model

Abhishek Mukhopadhyay, Boris H. Aguilar, Igor S. Tolokh, Alexey V. Onufriev
2014 Journal of Chemical Theory and Computation  
The proposed charge hydration asymmetric−generalized Born (CHA−GB) approximation introduces this effect into the popular generalized Born (GB) model.  ...  The strategy leads to finding a new set of intrinsic atomic radii optimized for CHA−GB; these radii show physically meaningful variation with the atom type, in contrast to the radii set optimized for GB  ...  Here, we apply the strategy to derive a CHA-aware analogue of the GB equation, which we call the charge hydration asymmetric−generalized Born (CHA−GB) model.  ... 
doi:10.1021/ct4010917 pmid:24803871 pmcid:PMC3985468 fatcat:vm5i5og5rrh6fh65l4bi47e7ki

Accurate and efficient generalized born model based on solvent accessibility: Derivation and application for LogP octanol/water prediction and flexible peptide docking

Maxim Totrov
2004 Journal of Computational Chemistry  
A novel method for fast and accurate evaluation of the generalized Born radii in macromolecular solvation electrostatics calculations is proposed, based on the solvent accessibility of the first two solvation  ...  The reverse generalized Born radii calculated by the method have correlation coefficient of 98.7% and RMSD of 0.031 Å Ϫ1 with the values obtained using a precise but significantly slower numerical boundary  ...  Discussion A method to calculate generalized Born radii based on the burial factors for the first two solvation layers is proposed.  ... 
doi:10.1002/jcc.10392 pmid:14735578 fatcat:5yftzqrgxjbtxj3zenktcmrkm4

A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation

Wei Cai, Zhenli Xu, Andrij Baumketner
2008 Journal of Computational Physics  
In this paper, a new method for calculating effective atomic radii within the generalized Born (GB) model of implicit solvation is proposed, for use in computer simulations of bio-molecules.  ...  First, a new formulation for the GB radii is developed, in which smooth kernels are used to eliminate the divergence in volume integrals intrinsic in the model.  ...  Michael Feig for bringing this interesting problem to the authors' attention and later discussions. Also, the authors thank Prof. Guowei Wei for sharing his molecular surface code during this work.  ... 
doi:10.1016/j.jcp.2008.08.015 pmid:20027201 pmcid:PMC2598740 fatcat:rczdr5squjcv7pbdekp33m2qgi

O(NlogN) Continuous electrostatics method for fast calculation of solvation energies of biomolecules

P. O. Fedichev, E. G. Getmantsev, L. I. Menshikov
2010 Journal of Computational Chemistry  
We report a development of a new fast surface-based method for numerical calculations of solvation energy of biomolecules with a large number of charged groups.  ...  field potential at any point, provides both the solvation energy and its derivatives suitable for Molecular Dynamics simulations.  ...  We report a development of a new fast surface-based method for numerical calculations of solvation energy of biomolecules with a large number of charged groups.  ... 
doi:10.1002/jcc.21719 pmid:21425292 fatcat:ownwzczxb5bzddqszvz3ciyiiq

Generalized Born forces: Surface integral formulation

Federico Fogolari, Alessandra Corazza, Gennaro Esposito
2013 Journal of Chemical Physics  
Generalized Born model based approaches Generalized Born (GB) models have emerged as a powerful alternative to PBE approaches.  ...  In this class of continuum models, the solvation energy is written as a sum of pairwise  ...  Lait is acknowledged for valuable support.  ... 
doi:10.1063/1.4789537 pmid:23406103 fatcat:ayjepfw2q5dvblobs3loh533se

What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules

Zhiyun Yu, Matthew P. Jacobson, Richard A. Friesner
2005 Journal of Computational Chemistry  
We have developed a version of our surface generalized Born (SGB) model that employs a Gaussian surface, as opposed to the van der Waals surface used previously.  ...  An efficient and robust algorithm is designed to construct and triangulate the Gaussian surface for large biomolecules with arbitrary shapes, and to compute the various terms required for energy gradients  ...  VSGB and DelPhi is roughly linear for small Born radii but then deviates sharply, with a bias towards smaller radii for atoms in the interior of the system (Born radii >7 Å), as we expected.  ... 
doi:10.1002/jcc.20307 pmid:16261581 pmcid:PMC2743414 fatcat:54yyfkypeffovmblydfvfa4ibu

Analytical electrostatics for biomolecules: Beyond the generalized Born approximation

Grigori Sigalov, Andrew Fenley, Alexey Onufriev
2006 Journal of Chemical Physics  
The new model is incorporated into the AMBER molecular modeling package and tested on small proteins.  ...  In the current work, we extend the method to biomolecules of arbitrary shape and provide computationally efficient algorithms for estimation of the parameters of the model.  ...  GB, and the reference NPB methods. 124902-7 Beyond the generalized Born approximation J.  ... 
doi:10.1063/1.2177251 pmid:16599720 fatcat:ifntasxmfrhcte22dhezpd5w6q

A Stochastic Technique that Computes Electrostatic Solvation and Binding Free Energies in the Generalized Born Model with Exact Born Radii

Robert C. Harris, Marcia O. Fenley
2012 Biophysical Journal  
We have developed a general approach to allow for these ionization states to change dynamically during the simulation.  ...  We anticipate that these methods will be useful for probing the photophysical mechanism of qE quenching and using the dynamics of NPQ induction as a probe of chloroplast dynamics. 832-Pos Board B618 The  ...  By solving 168a for the Born radii stochastically, the exact Born radii can be computed without the need for multiple expensive deterministic calculations.  ... 
doi:10.1016/j.bpj.2011.11.916 fatcat:yyhgh3s5qjfipg7aj722peuw3m

Fast Molecular Solvation Energetics and Forces Computation

Chandrajit Bajaj, Wenqi Zhao
2010 SIAM Journal on Scientific Computing  
In this paper we develop a fast surface-based generalized Born method to compute the electrostatic solvation energy along with the energy derivatives for the solvation forces.  ...  We also wish to thank several members of our CVC group for developing and maintaining TexMol, our molecular modeling and visualization software tool, which was used in conjunction with our nFFTGB implementation  ...  Rezaul Chowdhury for all the excellent suggestions that have resulted in a considerably improved paper.  ... 
doi:10.1137/090746173 pmid:20200598 pmcid:PMC2830669 fatcat:guaj4ocogvenlp2wrgjrkbixpa

The AGBNP2 Implicit Solvation Model [article]

Emilio Gallicchio, Kristina Paris, Ronald M. Levy (Rutgers University)
2009 arXiv   pre-print
We show that the new volumetric model produces Born radii and surface areas in good agreement with accurate numerical evaluations.  ...  This new component is added to the Generalized Born and non-polar AGBNP models which have been improved with respect to the description of the solute volume description.  ...  Methods The Analytical Generalized Born plus Non-Polar Implicit Solvent Model (AGBNP) In this section we briefly review the formulation of the AGBNP1 implicit solvent model, which forms the basis for  ... 
arXiv:0903.3058v1 fatcat:k5cauw6sz5ampitmdr2z5wexui

Do we have to explicitly model the ions in Brownian dynamics simulations of proteins?

Melanie J. Zimmer, Tihamér Geyer
2012 Journal of Chemical Physics  
Interesting new developments include more refined non-polar solvation energy estimators, and implicit methods for modeling low-dielectric and heterogeneous environments such as membrane systems.  ...  Recent methodological developments have mainly focused on the extension of the generalized Born (GB) formalism for variable dielectric environments and accurate treatment of nonpolar solvation.  ...  We propose two alternative approaches for atoms in the second group. The Born radii of these atoms may simply be computed by a fast GB method.  ... 
doi:10.1063/1.3698593 pmid:22462897 fatcat:i4ewhl25evf2zoesdifstzfgge

The AGBNP2 Implicit Solvation Model

Emilio Gallicchio, Kristina Paris, Ronald M. Levy
2009 Journal of Chemical Theory and Computation  
This new component is added to the generalized Born and nonpolar AGBNP terms.  ...  It is shown that the new volumetric model produces Born radii and surface areas in good agreement with accurate numerical evaluations of these quantities.  ...  Methods The Analytical Generalized Born plus Nonpolar Implicit Solvent Model (AGBNP).  ... 
doi:10.1021/ct900234u pmid:20419084 pmcid:PMC2857935 fatcat:kgimcxiujjdd7bektisktoknxu
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