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Items: 1 to 20 of 47

1.

All-atom empirical potential for molecular modeling and dynamics studies of proteins.

MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FT, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M.

J Phys Chem B. 1998 Apr 30;102(18):3586-616. doi: 10.1021/jp973084f.

PMID:
24889800
2.

Quantitative modeling of membrane deformations by multihelical membrane proteins: application to G-protein coupled receptors.

Mondal S, Khelashvili G, Shan J, Andersen OS, Weinstein H.

Biophys J. 2011 Nov 2;101(9):2092-101. doi: 10.1016/j.bpj.2011.09.037. Epub 2011 Nov 1.

3.

Solid-state NMR ensemble dynamics as a mediator between experiment and simulation.

Kim T, Jo S, Im W.

Biophys J. 2011 Jun 22;100(12):2922-8. doi: 10.1016/j.bpj.2011.02.063.

4.

Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables.

Jo S, Im W.

Biophys J. 2011 Jun 22;100(12):2913-21. doi: 10.1016/j.bpj.2011.05.009.

5.

Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. I: molecular dynamics simulations.

Ingólfsson HI, Li Y, Vostrikov VV, Gu H, Hinton JF, Koeppe RE 2nd, Roux B, Andersen OS.

J Phys Chem B. 2011 Jun 9;115(22):7417-26. doi: 10.1021/jp200904d. Epub 2011 May 16.

6.

Molecular dynamics studies of ion permeation in VDAC.

Rui H, Lee KI, Pastor RW, Im W.

Biophys J. 2011 Feb 2;100(3):602-10. doi: 10.1016/j.bpj.2010.12.3711.

7.

Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation.

Kim T, Im W.

Biophys J. 2010 Jul 7;99(1):175-83. doi: 10.1016/j.bpj.2010.04.015.

8.

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.

Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD Jr, Pastor RW.

J Phys Chem B. 2010 Jun 17;114(23):7830-43. doi: 10.1021/jp101759q.

9.

Screening for small molecules' bilayer-modifying potential using a gramicidin-based fluorescence assay.

Ingólfsson HI, Andersen OS.

Assay Drug Dev Technol. 2010 Aug;8(4):427-36. doi: 10.1089/adt.2009.0250.

10.

Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes.

Lundbaek JA, Collingwood SA, Ingólfsson HI, Kapoor R, Andersen OS.

J R Soc Interface. 2010 Mar 6;7(44):373-95. doi: 10.1098/rsif.2009.0443. Epub 2009 Nov 25. Review.

11.

CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes.

Jo S, Lim JB, Klauda JB, Im W.

Biophys J. 2009 Jul 8;97(1):50-8. doi: 10.1016/j.bpj.2009.04.013.

12.

CHARMM: the biomolecular simulation program.

Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M.

J Comput Chem. 2009 Jul 30;30(10):1545-614. doi: 10.1002/jcc.21287. Review.

13.

CHARMM-GUI: a web-based graphical user interface for CHARMM.

Jo S, Kim T, Iyer VG, Im W.

J Comput Chem. 2008 Aug;29(11):1859-65. doi: 10.1002/jcc.20945.

PMID:
18351591
14.

Transmembrane helix tilting: insights from calculating the potential of mean force.

Lee J, Im W.

Phys Rev Lett. 2008 Jan 11;100(1):018103. Epub 2008 Jan 8.

PMID:
18232823
15.
16.

Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers.

Cordomí A, Perez JJ.

J Phys Chem B. 2007 Jun 28;111(25):7052-63. Epub 2007 May 27.

PMID:
17530884
17.

Bilayer thickness and membrane protein function: an energetic perspective.

Andersen OS, Koeppe RE 2nd.

Annu Rev Biophys Biomol Struct. 2007;36:107-30. Review.

PMID:
17263662
18.

Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains.

Kucerka N, Tristram-Nagle S, Nagle JF.

J Membr Biol. 2005 Dec;208(3):193-202. Epub 2006 Apr 8.

PMID:
16604469
20.

Importance of tensor asymmetry for the analysis of 2H NMR spectra from deuterated aromatic rings.

Pulay P, Scherer EM, van der Wel PC, Koeppe RE 2nd.

J Am Chem Soc. 2005 Dec 14;127(49):17488-93.

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