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Items: 1 to 20 of 31


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

Arthur EJ, Brooks CL 3rd.

J Comput Chem. 2016 Apr 15;37(10):927-39. doi: 10.1002/jcc.24280.


Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins.

Nguyen H, PĂ©rez A, Bermeo S, Simmerling C.

J Chem Theory Comput. 2015 Aug 11;11(8):3714-28. doi: 10.1021/acs.jctc.5b00271.


Multidimensional persistence in biomolecular data.

Xia K, Wei GW.

J Comput Chem. 2015 Jul 30;36(20):1502-20. doi: 10.1002/jcc.23953.


Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents.

Bureau HR, Merz DR Jr, Hershkovits E, Quirk S, Hernandez R.

PLoS One. 2015 May 13;10(5):e0127034. doi: 10.1371/journal.pone.0127034.


Modulation of the disordered conformational ensembles of the p53 transactivation domain by cancer-associated mutations.

Ganguly D, Chen J.

PLoS Comput Biol. 2015 Apr 21;11(4):e1004247. doi: 10.1371/journal.pcbi.1004247.


Improved Generalized Born Solvent Model Parameters for Protein Simulations.

Nguyen H, Roe DR, Simmerling C.

J Chem Theory Comput. 2013 Apr 9;9(4):2020-2034.


Physical Modeling of Aqueous Solvation.

Fennell CJ, Dill KA.

J Stat Phys. 2011 Oct 1;145(2):209-226.


Measuring the shapes of macromolecules - and why it matters.

Li J, Mach P, Koehl P.

Comput Struct Biotechnol J. 2013 Dec 9;8:e201309001. doi: 10.5936/csbj.201309001. Review.


The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling.

Muddana HS, Sapra NV, Fenley AT, Gilson MK.

J Chem Phys. 2013 Jun 14;138(22):224504. doi: 10.1063/1.4808376.


Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations.

Kleinjung J, Scott WR, Allison JR, van Gunsteren WF, Fraternali F.

J Chem Theory Comput. 2012 Jul 10;8(7):2391-2403.


Coarse-Grained Molecular Models of Water: A Review.

Hadley KR, McCabe C.

Mol Simul. 2012 Jul;38(8-9):671-681.


Biomolecular dynamics: order-disorder transitions and energy landscapes.

Whitford PC, Sanbonmatsu KY, Onuchic JN.

Rep Prog Phys. 2012 Jul;75(7):076601. doi: 10.1088/0034-4885/75/7/076601.


Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods.

Chen TS, Keating AE.

Protein Sci. 2012 Jul;21(7):949-63. doi: 10.1002/pro.2096. Review.


Surveying implicit solvent models for estimating small molecule absolute hydration free energies.

Knight JL, Brooks CL 3rd.

J Comput Chem. 2011 Oct;32(13):2909-23. doi: 10.1002/jcc.21876.


Intrinsically disordered proteins in a physics-based world.

Click TH, Ganguly D, Chen J.

Int J Mol Sci. 2010;11(12):5292-309. doi: 10.3390/ijms11125292. Review.


Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects.

Lomize AL, Pogozheva ID, Mosberg HI.

J Chem Inf Model. 2011 Apr 25;51(4):918-29. doi: 10.1021/ci2000192.


An improved coarse-grained model of solvation and the hydrophobic effect.

Varilly P, Patel AJ, Chandler D.

J Chem Phys. 2011 Feb 21;134(7):074109. doi: 10.1063/1.3532939.


Differential geometry based solvation model II: Lagrangian formulation.

Chen Z, Baker NA, Wei GW.

J Math Biol. 2011 Dec;63(6):1139-200. doi: 10.1007/s00285-011-0402-z.


Biomolecularmodeling and simulation: a field coming of age.

Schlick T, Collepardo-Guevara R, Halvorsen LA, Jung S, Xiao X.

Q Rev Biophys. 2011 May;44(2):191-228. doi: 10.1017/S0033583510000284. Review.

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