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Items: 20

1.

Picosecond to Millisecond Structural Dynamics in Human Ubiquitin.

Lindorff-Larsen K, Maragakis P, Piana S, Shaw DE.

J Phys Chem B. 2016 Aug 25;120(33):8313-20. doi: 10.1021/acs.jpcb.6b02024. Epub 2016 May 9.

2.

Systematic validation of protein force fields against experimental data.

Lindorff-Larsen K, Maragakis P, Piana S, Eastwood MP, Dror RO, Shaw DE.

PLoS One. 2012;7(2):e32131. doi: 10.1371/journal.pone.0032131. Epub 2012 Feb 22. Erratum in: PLoS One. 2013;8(4). doi:10.1371/annotation/8301b5d4-1ba3-40e7-8fcd-3e169b967044.

3.

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation.

Lindorff-Larsen K, Trbovic N, Maragakis P, Piana S, Shaw DE.

J Am Chem Soc. 2012 Feb 29;134(8):3787-91. doi: 10.1021/ja209931w. Epub 2012 Feb 16.

PMID:
22339051
4.

Activation mechanism of the β2-adrenergic receptor.

Dror RO, Arlow DH, Maragakis P, Mildorf TJ, Pan AC, Xu H, Borhani DW, Shaw DE.

Proc Natl Acad Sci U S A. 2011 Nov 15;108(46):18684-9. doi: 10.1073/pnas.1110499108. Epub 2011 Oct 26.

5.

Pathway and mechanism of drug binding to G-protein-coupled receptors.

Dror RO, Pan AC, Arlow DH, Borhani DW, Maragakis P, Shan Y, Xu H, Shaw DE.

Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13118-23. doi: 10.1073/pnas.1104614108. Epub 2011 Jul 21.

6.

Atomic-level characterization of the structural dynamics of proteins.

Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W.

Science. 2010 Oct 15;330(6002):341-6. doi: 10.1126/science.1187409.

7.

Equipartition and the Calculation of Temperature in Biomolecular Simulations.

Eastwood MP, Stafford KA, Lippert RA, Jensen MØ, Maragakis P, Predescu C, Dror RO, Shaw DE.

J Chem Theory Comput. 2010 Jul 13;6(7):2045-58. doi: 10.1021/ct9002916.

PMID:
26615934
8.

Improved side-chain torsion potentials for the Amber ff99SB protein force field.

Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, Shaw DE.

Proteins. 2010 Jun;78(8):1950-8. doi: 10.1002/prot.22711.

9.

Principles of conduction and hydrophobic gating in K+ channels.

Jensen MØ, Borhani DW, Lindorff-Larsen K, Maragakis P, Jogini V, Eastwood MP, Dror RO, Shaw DE.

Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):5833-8. doi: 10.1073/pnas.0911691107. Epub 2010 Mar 15.

10.

Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations.

Wriggers W, Stafford KA, Shan Y, Piana S, Maragakis P, Lindorff-Larsen K, Miller PJ, Gullingsrud J, Rendleman CA, Eastwood MP, Dror RO, Shaw DE.

J Chem Theory Comput. 2009 Oct 13;5(10):2595-605. doi: 10.1021/ct900229u.

PMID:
26631775
11.

Gaussian-mixture umbrella sampling.

Maragakis P, van der Vaart A, Karplus M.

J Phys Chem B. 2009 Apr 9;113(14):4664-73. doi: 10.1021/jp808381s.

12.

Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise.

Maragakis P, Ritort F, Bustamante C, Karplus M, Crooks GE.

J Chem Phys. 2008 Jul 14;129(2):024102. doi: 10.1063/1.2937892.

13.

A differential fluctuation theorem.

Maragakis P, Spichty M, Karplus M.

J Phys Chem B. 2008 May 15;112(19):6168-74. doi: 10.1021/jp077037r. Epub 2008 Mar 11.

PMID:
18331019
14.

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins.

Maragakis P, Lindorff-Larsen K, Eastwood MP, Dror RO, Klepeis JL, Arkin IT, Jensen MØ, Xu H, Trbovic N, Friesner RA, Palmer AG III, Shaw DE.

J Phys Chem B. 2008 May 15;112(19):6155-8. doi: 10.1021/jp077018h. Epub 2008 Mar 1.

15.

Determination of DNA-base orientation on carbon nanotubes through directional optical absorbance.

Meng S, Wang WL, Maragakis P, Kaxiras E.

Nano Lett. 2007 Aug;7(8):2312-6. Epub 2007 Jul 3.

PMID:
17608443
16.

DNA nucleoside interaction and identification with carbon nanotubes.

Meng S, Maragakis P, Papaloukas C, Kaxiras E.

Nano Lett. 2007 Jan;7(1):45-50.

PMID:
17212438
17.

Optimal estimates of free energies from multistate nonequilibrium work data.

Maragakis P, Spichty M, Karplus M.

Phys Rev Lett. 2006 Mar 17;96(10):100602. Epub 2006 Mar 15. Erratum in: Phys Rev Lett. 2007 Jun 22;98(25):259901.

PMID:
16605720
18.

Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide.

Ren W, Vanden-Eijnden E, Maragakis P, E W.

J Chem Phys. 2005 Oct 1;123(13):134109.

PMID:
16223277
19.
20.

Carbon nanotube interaction with DNA.

Lu G, Maragakis P, Kaxiras E.

Nano Lett. 2005 May;5(5):897-900.

PMID:
15884890

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