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000155851 0247_ $$2doi$$a10.1021/ct500084y
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000155851 041__ $$aEnglish
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000155851 1001_ $$0P:(DE-HGF)0$$aCarballo-Pacheco, Martín$$b0
000155851 245__ $$aExtension of the FACTS Implicit Solvation Model to Membranes
000155851 260__ $$aWashington, DC$$bAmerican Chemical Society (ACS)$$c2014
000155851 3367_ $$0PUB:(DE-HGF)16$$2PUB:(DE-HGF)$$aJournal Article$$bjournal$$mjournal$$s1417708451_21921
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000155851 520__ $$aThe generalized Born (GB) formalism can be used to model water as a dielectric continuum. Among the different implicit solvent models using the GB formalism, FACTS is one of the fastest. Here, we extend FACTS so that it can represent a membrane environment. This extension is accomplished by considering a position dependent dielectric constant and empirical surface tension parameter. For the calculation of the effective Born radii in different dielectric environments we present a parameter-free approximation to Kirkwood’s equation, which uses the Born radii obtained with FACTS for the water environment as input. This approximation is tested for the calculation of self-free energies, pairwise interaction energies in solution and solvation free energies of complete protein conformations. The results compare well to those from the finite difference Poisson method. The new implicit membrane model is applied to estimate free energy insertion profiles of amino acid analogues and in molecular dynamics simulations of melittin, WALP23 and KALP23, glycophorin A, bacteriorhodopsin, and a Clc channel dimer. In all cases, the results agree qualitatively with experiments and explicit solvent simulations. Moreover, the implicit membrane model is only six times slower than a vacuum simulation.
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000155851 7001_ $$0P:(DE-HGF)0$$aVancea, Ioan$$b1
000155851 7001_ $$0P:(DE-Juel1)132024$$aStrodel, Birgit$$b2$$eCorresponding Author$$ufzj
000155851 773__ $$0PERI:(DE-600)2166976-4$$a10.1021/ct500084y$$gVol. 10, no. 8, p. 3163 - 3176$$n8$$p3163 - 3176$$tJournal of chemical theory and computation$$v10$$x1549-9626$$y2014
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000155851 9101_ $$0I:(DE-588b)5008462-8$$6P:(DE-Juel1)132024$$aForschungszentrum Jülich GmbH$$b2$$kFZJ
000155851 9132_ $$0G:(DE-HGF)POF3-553$$1G:(DE-HGF)POF3-550$$2G:(DE-HGF)POF3-500$$aDE-HGF$$bKey Technologies$$lBioSoft – Fundamentals for future Technologies in the fields of Soft Matter and Life Sciences$$vPhysical Basis of Diseases$$x0
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000155851 9141_ $$y2014
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