Protein simulations combining an all-atom force field with a Go term

被引：14

作者：

Meinke, Jan H.

Hansmann, Ulrich H. E.

机构：

[1] Forschungszentrum Julich, John Von Neumann Inst Comp, D-52425 Julich, Germany

[2] Michigan Technol Univ, Dept Phys, Houghton, MI 49931 USA

来源：

JOURNAL OF PHYSICS-CONDENSED MATTER | 2007年 / 19卷 / 28期

关键词：

D O I：

10.1088/0953-8984/19/28/285215

中图分类号：

O469 [凝聚态物理学];

学科分类号：

070205 ;

摘要：

Using a variant of parallel tempering, we study the changes in sampling within a simulation, when the all- atom model is coupled to a Go- like potential. We find that the native structure is not the lowest- energy configuration in the all- atom force field. Adding a Go term deforms the energy landscape in such a way that the native configuration becomes the global minimum but does not lead to faster thermalization.

引用

页数：9

共 50 条

[41] An all-atom force field for tertiary structure prediction of helical proteins [J].

Herges, T ;

Wenzel, W .

BIOPHYSICAL JOURNAL, 2004, 87 (05) :3100-3109

[42] All-atom Molecular Dynamics Simulations of a Membrane Protein Stabilizing Polymer [J].

Drasler, William J. ;

Sachs, Jonathan N. .

BIOPHYSICAL JOURNAL, 2009, 96 (03) :41A-41A

[43] Adsorption of Protein on a Au Surface Studied by All-Atom Atomistic Simulations [J].

Wei, Aoran ;

Deng, Chuang .

JOURNAL OF PHYSICAL CHEMISTRY C, 2016, 120 (24) :13103-13112

[44] CHARMM all-atom additive force field for carbohydrates: Parameter optimization overview and utilization for simulations of heterogeneous systems [J].

MacKerell, Alexander D., Jr. ;

Guvench, Olgun ;

Mallajosyula, Sairam S. ;

Hatcher, Elizabeth R. ;

Raman, Prabhu .

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2011, 241

[45] Protein sidechain rotamer prediction using an all-atom force field/implicit solvent model. [J].

Jacobson, M ;

Friesner, RA .

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2001, 222 :U415-U415

[46] Ab initio prediction of protein structure with an off-lattice all-atom force field. [J].

Scheraga, HA ;

Vila, JA ;

Ripoll, DR .

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2004, 227 :U342-U342

[47] Examining the Origins of the Hydration Force Between Lipid Bilayers Using All-Atom Simulations [J].

Anastasia N. Gentilcore ;

Naveen Michaud-Agrawal ;

Paul S. Crozier ;

Mark J. Stevens ;

Thomas B. Woolf .

Journal of Membrane Biology, 2010, 235 :1-15

[48] H-bond network optimization in protein-protein complexes: Are all-atom force field scores enough? [J].

Masone, Diego ;

Cabeza de Vaca, Israel ;

Pons, Carles ;

Fernandez Recio, Juan ;

Guallar, Victor .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2012, 80 (03) :818-824

[49] Accelerating all-atom protein folding simulations through reduced dihedral barriers [J].

Endres, RG .

MOLECULAR SIMULATION, 2005, 31 (11) :773-777

[50] Physical Properties at the Base for the Development of an All-Atom Force Field for Ethylene Glycol [J].

Szefczyk, Borys ;

Cordeiro, M. Natalia D. S. .

JOURNAL OF PHYSICAL CHEMISTRY B, 2011, 115 (12) :3013-3019

← 1 2 3 4 5 →