| Revised RNA dihedral parameters for the amber force field improve RNA molecular dynamics AH Aytenfisu, A Spasic, A Grossfield, HA Stern, DH Mathews Journal of chemical theory and computation 13 (2), 900-915, 2017 | 112 | 2017 |
| Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics JA Liberman, KC Suddala, A Aytenfisu, D Chan, IA Belashov, M Salim, ... Proceedings of the National Academy of Sciences 112 (27), E3485-E3494, 2015 | 76 | 2015 |
| CHARMM drude polarizable force field for glycosidic linkages involving pyranoses and furanoses AH Aytenfisu, M Yang, AD MacKerell Jr Journal of chemical theory and computation 14 (6), 3132-3143, 2018 | 35 | 2018 |
| Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics AH Aytenfisu, JA Liberman, JE Wedekind, DH Mathews Rna 21 (11), 1898-1907, 2015 | 25 | 2015 |
| Modified AMBER force field correctly models the conformational preference for tandem GA pairs in RNA AH Aytenfisu, A Spasic, MG Seetin, J Serafini, DH Mathews Journal of Chemical Theory and Computation 10 (3), 1292-1301, 2014 | 23 | 2014 |
| Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides AA Kognole, AH Aytenfisu, AD MacKerell Journal of molecular modeling 26, 1-11, 2020 | 22 | 2020 |
| Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives P Pandey, AH Aytenfisu, AD MacKerell Jr, SS Mallajosyula Journal of chemical theory and computation 15 (9), 4982-5000, 2019 | 21 | 2019 |
| Impact of electronic polarizability on protein-functional group interactions H Goel, W Yu, VD Ustach, AH Aytenfisu, D Sun, AD MacKerell Physical Chemistry Chemical Physics 22 (13), 6848-6860, 2020 | 20 | 2020 |
| Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates MC Small, AH Aytenfisu, FY Lin, X He, AMKJ D. Journal of Computer-Aided Molecular Design, 2017 | 20 | 2017 |
| Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field M Yang, AH Aytenfisu, AD MacKerell Jr Carbohydrate research 457, 41-50, 2018 | 19 | 2018 |
| Site-selective chemoenzymatic modification on the core fucose of an antibody enhances its Fcγ receptor affinity and ADCC activity C Li, G Chong, G Zong, DA Knorr, S Bournazos, AH Aytenfisu, GK Henry, ... Journal of the American Chemical Society 143 (20), 7828-7838, 2021 | 16 | 2021 |
| Impact of branching on the conformational heterogeneity of the lipopolysaccharide from Klebsiella pneumoniae: Implications for vaccine design AH Aytenfisu, R Simon, AD MacKerell Jr Carbohydrate research 475, 39-47, 2019 | 9 | 2019 |
| Insights into substrate recognition and specificity for IgG by Endoglycosidase S2 AH Aytenfisu, D Deredge, EH Klontz, J Du, EJ Sundberg, AD MacKerell Jr PLoS Computational Biology 17 (7), e1009103, 2021 | 7 | 2021 |
| Extension of the charmm classical drude polarizable force field to n-and o-linked glycopeptides and glycoproteins AA Kognole, AH Aytenfisu, AD MacKerell Jr The Journal of Physical Chemistry B 126 (35), 6642-6653, 2022 | 6 | 2022 |
| Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields A Ruda, AH Aytenfisu, TA d’Ortoli, AD MacKerell, G Widmalm Physical Chemistry Chemical Physics 25 (4), 3042-3060, 2023 | 5 | 2023 |
| Development of CHARMM Additive Potential Energy Parameters for α-Methyl Amino Acids AJ Pane, W Yu, A Aytenfisu, J Tunyi, RM Venable, AD MacKerell Jr, ... The Journal of Physical Chemistry B 125 (42), 11687-11696, 2021 | | 2021 |
David H. MathewsDepartment of Biochemistry and Biophysics, University of Rochester Medical CenterVerified email at urmc.rochester.edu
