Insights into substrate recognition and specificity for IgG by Endoglycosidase S2 von Aytenfisu, Asaminew H, Deredge, Daniel, Klontz, Erik H, Du, Jonathan, Sundberg, Eric J, MacKerell, Alexander D

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Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics von Aytenfisu, Asaminew H, Spasic, Aleksandar, Grossfield, Alan, Stern, Harry A, Mathews, David H

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Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O‑Linked Glycopeptides and Glycoproteins von Kognole, Abhishek A., Aytenfisu, Asaminew H., MacKerell, Alexander D.

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CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses von Aytenfisu, Asaminew H, Yang, Mingjun, MacKerell, Alexander D

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Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields von Ruda, Alessandro, Aytenfisu, Asaminew H, Angles d'Ortoli, Thibault, MacKerell, Alexander D, Widmalm, Göran

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Drude Polarizable Force Field Parametrization of Carboxylate and N‑Acetyl Amine Carbohydrate Derivatives von Pandey, Poonam, Aytenfisu, Asaminew H, MacKerell, Alexander D, Mallajosyula, Sairam S

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Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field von Yang, Mingjun, Aytenfisu, Asaminew H., MacKerell, Alexander D.

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Development of CHARMM additive potential energy parameters for α-methyl amino acids von Pane, Anthony J., Yu, Wenbo, Aytenfisu, Asaminew H., Tunyi, Achombom (Jude), Venable, Richard M., MacKerell, Alexander D., Pastor, Richard W.

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Impact of electronic polarizability on protein-functional group interactions von Goel, Himanshu, Yu, Wenbo, Ustach, Vincent D, Aytenfisu, Asaminew H, Sun, Delin, MacKerell, Alexander D

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Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides von Kognole, Abhishek A., Aytenfisu, Asaminew H., MacKerell, Alexander D.

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Impact of branching on the conformational heterogeneity of the lipopolysaccharide from Klebsiella pneumoniae: Implications for vaccine design von Aytenfisu, Asaminew H., Simon, Raphael, MacKerell, Alexander D.

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Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics von Aytenfisu, Asaminew H, Liberman, Joseph A, Wedekind, Joseph E, Mathews, David H

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Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates von Small, Meagan C., Aytenfisu, Asaminew H., Lin, Fang-Yu, He, Xibing, MacKerell, Alexander D.

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Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA von Aytenfisu, Asaminew H, Spasic, Aleksandar, Seetin, Matthew G, Serafini, John, Mathews, David H

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Impact of Branching on the Conformational Heterogeneity of the Lipopolysaccharide from Klebsiella Pneumonia: Implications for Vaccine Design von Aytenfisu, Asaminew H., Simon, Raphael, MacKerell, Alexander D.

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Antibody Modeling using Molecular Dynamics and Silcs Fragmaps von Aytenfisu, Asaminew H., Deredge, Daniel J., Klontz, Erik H., Du, Jonathan, Sundberg, Eric J., MacKerell, Alexander D.

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Molecular mechanism for preQ 1 -II riboswitch function revealed by molecular dynamics von Aytenfisu, Asaminew H., Liberman, Joseph A., Wedekind, Joseph E., Mathews, David H.

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Molecular mechanism for preQ sub(1)-II riboswitch function revealed by molecular dynamics von Aytenfisu, Asaminew H, Liberman, Joseph A, Wedekind, Joseph E, Mathews, David H

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Structural analysis of a class III preQ₁ riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics von Liberman, Joseph A., Suddala, Krishna C., Aytenfisu, Asaminew, Chan, Dalen, Belashov, Ivan A., Salim, Mohammad, Mathews, David H., Spitale, Robert C., Walter, Nils G., Wedekind, Joseph E.

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Structural analysis of a class III preQ^sub 1^ riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics von Liberman, Joseph A, Suddala, Krishna C, Aytenfisu, Asaminew, Chan, Dalen, Belashov, Ivan A, Salim, Mohammad, Mathews, David H, Spitale, Robert C, Walter, Nils G, Wedekind, Joseph E

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