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Items: 1 to 20 of 76


Chemically accurate coarse graining of double-stranded DNA.

Savelyev A, Papoian GA.

Proc Natl Acad Sci U S A. 2010 Nov 23;107(47):20340-5. doi: 10.1073/pnas.1001163107. Epub 2010 Nov 8.


Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems.

Kamerlin SC, Vicatos S, Dryga A, Warshel A.

Annu Rev Phys Chem. 2011;62:41-64. doi: 10.1146/annurev-physchem-032210-103335. Review.


On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes.

Rychkova A, Vicatos S, Warshel A.

Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17598-603. doi: 10.1073/pnas.1012207107. Epub 2010 Sep 27.


Polarizable water model for the coarse-grained MARTINI force field.

Yesylevskyy SO, Schäfer LV, Sengupta D, Marrink SJ.

PLoS Comput Biol. 2010 Jun 10;6(6):e1000810. doi: 10.1371/journal.pcbi.1000810.


At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Kamerlin SC, Warshel A.

Proteins. 2010 May 1;78(6):1339-75. doi: 10.1002/prot.22654. Review.


Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39).

Voelz VA, Bowman GR, Beauchamp K, Pande VS.

J Am Chem Soc. 2010 Feb 10;132(5):1526-8. doi: 10.1021/ja9090353.


Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models.

Messer BM, Roca M, Chu ZT, Vicatos S, Kilshtain AV, Warshel A.

Proteins. 2010 Apr;78(5):1212-27. doi: 10.1002/prot.22640.


Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction.

Major DT, Heroux A, Orville AM, Valley MP, Fitzpatrick PF, Gao J.

Proc Natl Acad Sci U S A. 2009 Dec 8;106(49):20734-9. doi: 10.1073/pnas.0911416106. Epub 2009 Nov 19.


Protein contents in biological membranes can explain abnormal solvation of charged and polar residues.

Johansson AC, Lindahl E.

Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15684-9. doi: 10.1073/pnas.0905394106. Epub 2009 Sep 1.


Enzyme millisecond conformational dynamics do not catalyze the chemical step.

Pisliakov AV, Cao J, Kamerlin SC, Warshel A.

Proc Natl Acad Sci U S A. 2009 Oct 13;106(41):17359-64. doi: 10.1073/pnas.0909150106. Epub 2009 Sep 25.


Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases.

Liu H, Shi Y, Chen XS, Warshel A.

Proc Natl Acad Sci U S A. 2009 May 5;106(18):7449-54. doi: 10.1073/pnas.0900532106. Epub 2009 Apr 21.


Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information.

Calderon CP, Janosi L, Kosztin I.

J Chem Phys. 2009 Apr 14;130(14):144908. doi: 10.1063/1.3106225.


Systematic multiscale simulation of membrane protein systems.

Ayton GS, Voth GA.

Curr Opin Struct Biol. 2009 Apr;19(2):138-44. doi: 10.1016/ Epub 2009 Apr 9. Review.


Toward accurate screening in computer-aided enzyme design.

Roca M, Vardi-Kilshtain A, Warshel A.

Biochemistry. 2009 Apr 14;48(14):3046-56. doi: 10.1021/bi802191b.


On the relationship between folding and chemical landscapes in enzyme catalysis.

Roca M, Messer B, Hilvert D, Warshel A.

Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):13877-82. doi: 10.1073/pnas.0803405105. Epub 2008 Sep 8.


Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase.

Pisliakov AV, Sharma PK, Chu ZT, Haranczyk M, Warshel A.

Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7726-31. doi: 10.1073/pnas.0800580105. Epub 2008 May 28.


Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution.

Rosta E, Haranczyk M, Chu ZT, Warshel A.

J Phys Chem B. 2008 May 8;112(18):5680-92. doi: 10.1021/jp711496y. Epub 2008 Apr 16.

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