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Items: 8


Impact of branching on the conformational heterogeneity of the lipopolysaccharide from Klebsiella pneumoniae: Implications for vaccine design.

Aytenfisu AH, Simon R, MacKerell AD Jr.

Carbohydr Res. 2019 Mar 1;475:39-47. doi: 10.1016/j.carres.2019.02.003. Epub 2019 Feb 18.


CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses.

Aytenfisu AH, Yang M, MacKerell AD Jr.

J Chem Theory Comput. 2018 Jun 12;14(6):3132-3143. doi: 10.1021/acs.jctc.8b00175. Epub 2018 May 4.


Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field.

Yang M, Aytenfisu AH, MacKerell AD Jr.

Carbohydr Res. 2018 Mar 2;457:41-50. doi: 10.1016/j.carres.2018.01.004. Epub 2018 Jan 31.


Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates.

Small MC, Aytenfisu AH, Lin FY, He X, MacKerell AD Jr.

J Comput Aided Mol Des. 2017 Apr;31(4):349-363. doi: 10.1007/s10822-017-0010-0. Epub 2017 Feb 11.


Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.

Aytenfisu AH, Spasic A, Grossfield A, Stern HA, Mathews DH.

J Chem Theory Comput. 2017 Feb 14;13(2):900-915. doi: 10.1021/acs.jctc.6b00870. Epub 2017 Jan 24.


Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics.

Aytenfisu AH, Liberman JA, Wedekind JE, Mathews DH.

RNA. 2015 Nov;21(11):1898-907. doi: 10.1261/rna.051367.115. Epub 2015 Sep 14.


Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics.

Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3485-94. doi: 10.1073/pnas.1503955112. Epub 2015 Jun 23.


Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA.

Aytenfisu AH, Spasic A, Seetin MG, Serafini J, Mathews DH.

J Chem Theory Comput. 2014 Mar 11;10(3):1292-1301. Epub 2014 Jan 22.

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