A strategy for reducing gross errors in the generalized Born models of implicit solvation.

PubWeight™: 0.87‹?›

🔗 View Article (PMC 3100913)

Published in J Chem Phys on April 28, 2011

Authors

Alexey V Onufriev1, Grigori Sigalov

Author Affiliations

1: Department of Computer Science, 2050 Torgersen Hall, Virginia Tech, Blacksburg, Virginia 24061, USA. alexey@cs.vt.edu

Articles cited by this

Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A (2001) 42.14

Classical electrostatics in biology and chemistry. Science (1995) 17.26

Reduced surface: an efficient way to compute molecular surfaces. Biopolymers (1996) 10.62

Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins (2004) 9.15

Generalized born models of macromolecular solvation effects. Annu Rev Phys Chem (2000) 6.55

All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc (2002) 4.99

Generalized born model with a simple smoothing function. J Comput Chem (2003) 4.36

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem (2004) 3.83

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J Comput Chem (2003) 3.81

Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem (2002) 3.43

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water? Proc Natl Acad Sci U S A (2002) 3.41

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J Comput Chem (2004) 3.39

Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins. Proc Natl Acad Sci U S A (2003) 3.34

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proc Natl Acad Sci U S A (2006) 3.30

Effective Born radii in the generalized Born approximation: the importance of being perfect. J Comput Chem (2002) 3.06

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J Mol Biol (2002) 2.73

Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. J Am Chem Soc (2006) 2.59

Constant-pH molecular dynamics using continuous titration coordinates. Proteins (2004) 2.52

Constant pH molecular dynamics in generalized Born implicit solvent. J Comput Chem (2004) 2.43

Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins (2003) 2.39

Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent. Proc Natl Acad Sci U S A (2003) 2.31

Implicit solvation based on generalized Born theory in different dielectric environments. J Chem Phys (2004) 2.00

Ab initio folding of helix bundle proteins using molecular dynamics simulations. J Am Chem Soc (2003) 1.86

FACTS: Fast analytical continuum treatment of solvation. J Comput Chem (2008) 1.79

Theory of electrostatic interactions in macromolecules. Curr Opin Struct Biol (1995) 1.70

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation. J Phys Chem B (2007) 1.43

Linking folding with aggregation in Alzheimer's beta-amyloid peptides. Proc Natl Acad Sci U S A (2007) 1.42

Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. J Am Chem Soc (2009) 1.40

Protein molecular dynamics with the generalized Born/ACE solvent model. Proteins (2001) 1.35

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation. J Phys Chem B (2007) 1.28

Analytical electrostatics for biomolecules: beyond the generalized Born approximation. J Chem Phys (2006) 1.26

GBr(6): a parameterization-free, accurate, analytical generalized born method. J Phys Chem B (2007) 1.16

Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation. Proteins (2003) 1.06

Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: all-atom molecular dynamics in implicit solvent. J Comput Chem (2007) 1.02

An analytical approach to computing biomolecular electrostatic potential. II. Validation and applications. J Chem Phys (2008) 0.98

An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis. J Chem Phys (2008) 0.97

Calculations of proton-binding thermodynamics in proteins. Methods Enzymol (1998) 0.95

Analysis of integral expressions for effective Born radii. J Chem Phys (2007) 0.95

All-atom level direct folding simulation of a betabetaalpha miniprotein. J Chem Phys (2008) 0.84