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Results: 1 to 20 of 36

References for PMC Articles for PubMed (Select 21047091)

1.

Molecular dynamics free energy calculations to assess the possibility of water existence in protein nonpolar cavities.

Oikawa M, Yonetani Y.

Biophys J. 2010 Jun 16;98(12):2974-83. doi: 10.1016/j.bpj.2010.01.029.

2.

A review about nothing: are apolar cavities in proteins really empty?

Matthews BW, Liu L.

Protein Sci. 2009 Mar;18(3):494-502. doi: 10.1002/pro.61. Review.

3.

Water in nonpolar confinement: from nanotubes to proteins and beyond.

Rasaiah JC, Garde S, Hummer G.

Annu Rev Phys Chem. 2008;59:713-40. Review.

PMID:
18092942
4.

The entropic cost of bound water in crystals and biomolecules.

Dunitz JD.

Science. 1994 Apr 29;264(5159):670. No abstract available.

PMID:
17737951
5.

Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion.

Yin H, Hummer G, Rasaiah JC.

J Am Chem Soc. 2007 Jun 13;129(23):7369-77. Epub 2007 May 18.

PMID:
17508748
6.
7.

Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography.

Collins MD, Quillin ML, Hummer G, Matthews BW, Gruner SM.

J Mol Biol. 2007 Mar 30;367(3):752-63. Epub 2006 Dec 15.

8.

Determination of solvent content in cavities in IL-1beta using experimentally phased electron density.

Quillin ML, Wingfield PT, Matthews BW.

Proc Natl Acad Sci U S A. 2006 Dec 26;103(52):19749-53. Epub 2006 Dec 18.

9.

Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation.

Collins MD, Hummer G, Quillin ML, Matthews BW, Gruner SM.

Proc Natl Acad Sci U S A. 2005 Nov 15;102(46):16668-71. Epub 2005 Nov 3. Erratum in: Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4793.

10.

The Amber biomolecular simulation programs.

Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ.

J Comput Chem. 2005 Dec;26(16):1668-88.

11.

Water clusters in nonpolar cavities.

Vaitheeswaran S, Yin H, Rasaiah JC, Hummer G.

Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):17002-5. Epub 2004 Nov 30.

12.

Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes.

Vaitheeswaran S, Rasaiah JC, Hummer G.

J Chem Phys. 2004 Oct 22;121(16):7955-65.

PMID:
15485258
13.

Hydration free energies and entropies for water in protein interiors.

Olano LR, Rick SW.

J Am Chem Soc. 2004 Jun 30;126(25):7991-8000.

PMID:
15212549
14.

MHC-peptide binding is assisted by bound water molecules.

Petrone PM, Garcia AE.

J Mol Biol. 2004 Apr 23;338(2):419-35.

PMID:
15066441
15.

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P.

J Comput Chem. 2003 Dec;24(16):1999-2012.

PMID:
14531054
16.

Water conduction through the hydrophobic channel of a carbon nanotube.

Hummer G, Rasaiah JC, Noworyta JP.

Nature. 2001 Nov 8;414(6860):188-90.

PMID:
11700553
17.

Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations.

Peter C, Daura X, van Gunsteren WF.

J Biomol NMR. 2001 Aug;20(4):297-310.

PMID:
11563554
18.

Crystal structure of a naturally occurring parallel right-handed coiled coil tetramer.

Stetefeld J, Jenny M, Schulthess T, Landwehr R, Engel J, Kammerer RA.

Nat Struct Biol. 2000 Sep;7(9):772-6.

PMID:
10966648
19.

Water penetration and escape in proteins.

GarcĂ­a AE, Hummer G.

Proteins. 2000 Feb 15;38(3):261-72.

PMID:
10713987
20.

Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography.

Yu B, Blaber M, Gronenborn AM, Clore GM, Caspar DL.

Proc Natl Acad Sci U S A. 1999 Jan 5;96(1):103-8.

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