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Results: 1 to 20 of 104

1.

Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations.

Kortkhonjia E, Brandman R, Zhou JZ, Voelz VA, Chorny I, Kabakoff B, Patapoff TW, Dill KA, Swartz TE.

MAbs. 2013 Mar-Apr;5(2):306-22. doi: 10.4161/mabs.23651. Epub 2013 Feb 8.

PMID:
23396076
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Construction, MD simulation, and hydrodynamic validation of an all-atom model of a monoclonal IgG antibody.

Brandt JP, Patapoff TW, Aragon SR.

Biophys J. 2010 Aug 4;99(3):905-13. doi: 10.1016/j.bpj.2010.05.003.

PMID:
20682269
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug 2;10(4):040301. [Epub ahead of print]

PMID:
23912807
[PubMed - as supplied by publisher]
4.

Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone.

Murarka RK, Liwo A, Scheraga HA.

J Chem Phys. 2007 Oct 21;127(15):155103.

PMID:
17949219
[PubMed - indexed for MEDLINE]
5.

Dynamics of nuclear receptor Helix-12 switch of transcription activation by modeling time-resolved fluorescence anisotropy decays.

Batista MR, Martínez L.

Biophys J. 2013 Oct 1;105(7):1670-80. doi: 10.1016/j.bpj.2013.07.032.

PMID:
24094408
[PubMed - indexed for MEDLINE]
6.

Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations.

Riniker S, Eichenberger AP, van Gunsteren WF.

Eur Biophys J. 2012 Aug;41(8):647-61. doi: 10.1007/s00249-012-0837-1. Epub 2012 Jul 14.

PMID:
22797564
[PubMed - indexed for MEDLINE]
7.

Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor.

Doruker P, Atilgan AR, Bahar I.

Proteins. 2000 Aug 15;40(3):512-24.

PMID:
10861943
[PubMed - indexed for MEDLINE]
8.

Disulfide scrambling in IgG2 monoclonal antibodies: insights from molecular dynamics simulations.

Wang X, Kumar S, Singh SK.

Pharm Res. 2011 Dec;28(12):3128-44. doi: 10.1007/s11095-011-0503-9. Epub 2011 Jun 14.

PMID:
21671135
[PubMed - indexed for MEDLINE]
9.

Molecular dynamics of tryptophan in ribonuclease-T1. II. Correlations with fluorescence.

Axelsen PH, Prendergast FG.

Biophys J. 1989 Jul;56(1):43-66.

PMID:
2502198
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Exploring the energy landscape of antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition.

Thielges MC, Zimmermann J, Yu W, Oda M, Romesberg FE.

Biochemistry. 2008 Jul 8;47(27):7237-47. doi: 10.1021/bi800374q. Epub 2008 Jun 13.

PMID:
18549243
[PubMed - indexed for MEDLINE]
12.

Excipients differentially influence the conformational stability and pretransition dynamics of two IgG1 monoclonal antibodies.

Thakkar SV, Joshi SB, Jones ME, Sathish HA, Bishop SM, Volkin DB, Middaugh CR.

J Pharm Sci. 2012 Sep;101(9):3062-77. doi: 10.1002/jps.23187. Epub 2012 May 11.

PMID:
22581714
[PubMed - indexed for MEDLINE]
13.

NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations.

Xia J, Deng NJ, Levy RM.

J Phys Chem B. 2013 Jun 6;117(22):6625-34. doi: 10.1021/jp400797y. Epub 2013 May 28.

PMID:
23638941
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Conformational flexibility of the ErbB2 ectodomain and trastuzumab antibody complex as revealed by molecular dynamics and principal component analysis.

Franco-Gonzalez JF, Cruz VL, Ramos J, Martínez-Salazar J.

J Mol Model. 2013 Mar;19(3):1227-36. doi: 10.1007/s00894-012-1661-3. Epub 2012 Nov 17.

PMID:
23160933
[PubMed - indexed for MEDLINE]
15.

A direct coupling between global and internal motions in a single domain protein? MD investigation of extreme scenarios.

Hamaneh MB, Zhang L, Buck M.

Biophys J. 2011 Jul 6;101(1):196-204. doi: 10.1016/j.bpj.2011.05.041.

PMID:
21723830
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Conformational dynamics of cytochrome c: correlation to hydrogen exchange.

García AE, Hummer G.

Proteins. 1999 Aug 1;36(2):175-91.

PMID:
10398365
[PubMed - indexed for MEDLINE]
17.

Simulation of fluorescence anisotropy experiments: probing protein dynamics.

Schröder GF, Alexiev U, Grubmüller H.

Biophys J. 2005 Dec;89(6):3757-70. Epub 2005 Sep 16.

PMID:
16169987
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Molecular dynamics simulations of domain motions of substrate-free S-adenosyl- L-homocysteine hydrolase in solution.

Hu C, Fang J, Borchardt RT, Schowen RL, Kuczera K.

Proteins. 2008 Apr;71(1):131-43.

PMID:
17932938
[PubMed - indexed for MEDLINE]
19.

The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations.

Sgourakis NG, Garcia AE.

J Mol Biol. 2010 Apr 23;398(1):161-73. doi: 10.1016/j.jmb.2010.02.032. Epub 2010 Feb 23.

PMID:
20184892
[PubMed - indexed for MEDLINE]

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