| Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields C Bergonzo, NM Henriksen, DR Roe, TE Cheatham RNA 21 (9), 1578-1590, 2015 | 145 | 2015 |
| Multidimensional replica exchange molecular dynamics yields a converged ensemble of an RNA tetranucleotide C Bergonzo, NM Henriksen, DR Roe, JM Swails, AE Roitberg, ... Journal of chemical theory and computation 10 (1), 492-499, 2014 | 141 | 2014 |
| Improved Force Field Parameters Lead to a Better Description of RNA Structure C Bergonzo, TEC III Journal of Chemical Theory and Computation 11 (9), 3969-3972, 2015 | 140 | 2015 |
| Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods DR Roe, C Bergonzo, TE Cheatham III The Journal of Physical Chemistry B 118 (13), 3543-3552, 2014 | 111 | 2014 |
| An improved reaction coordinate for nucleic acid base flipping studies K Song, AJ Campbell, C Bergonzo, C de los Santos, AP Grollman, ... Journal of Chemical Theory and Computation 5 (11), 3105-3113, 2009 | 70 | 2009 |
| A partial nudged elastic band implementation for use with large or explicitly solvated systems C Bergonzo, AJ Campbell, RC Walker, C Simmerling International journal of quantum chemistry 109 (15), 3781-3790, 2009 | 63 | 2009 |
| Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition NA Kuznetsov, C Bergonzo, AJ Campbell, H Li, GV Mechetin, ... Nucleic acids research 43 (1), 272-281, 2015 | 56 | 2015 |
| Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics C Bergonzo, KB Hall, TE Cheatham III Journal of chemical theory and computation 12 (7), 3382-3389, 2016 | 49 | 2016 |
| Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase C Bergonzo, AJ Campbell, C de los Santos, AP Grollman, C Simmerling Journal of the American Chemical Society 133 (37), 14504-14506, 2011 | 45 | 2011 |
| DNA deformation-coupled recognition of 8-oxoguanine: conformational kinetic gating in human DNA glycosylase H Li, AV Endutkin, C Bergonzo, L Fu, A Grollman, DO Zharkov, ... Journal of the American Chemical Society 139 (7), 2682-2692, 2017 | 38 | 2017 |
| A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine–DNA glycosylase H Li, AV Endutkin, C Bergonzo, AJ Campbell, C de los Santos, ... Nucleic acids research 44 (2), 683-694, 2016 | 26 | 2016 |
| Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg2+ Bound Structure in the Presence of Monovalent Ions C Bergonzo, KB Hall, TE Cheatham III The Journal of Physical Chemistry B 119 (38), 12355-12364, 2015 | 25 | 2015 |
| Molecular Modeling of Nucleic Acid Structure R Galindo‐Murillo, C Bergonzo, TE Cheatham Current Protocols in Nucleic Acid Chemistry, 7.5. 1-7.5. 13, 2013 | 22* | 2013 |
| Structural Insights into DNA-Stabilized Silver Clusters D Schultz, RG Brinson, N Sari, JA Fagan, C Bergonzo, NJ Lin, JP Dunkers Soft Matter, 2019 | 15 | 2019 |
| Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments C Bergonzo, A Grishaev, S Bottaro RNA 28 (7), 937-946, 2022 | 14 | 2022 |
| Characterization of the internal translation initiation region in monoclonal antibodies expressed in Escherichia coli EM Leith, WB O'Dell, N Ke, C McClung, M Berkmen, C Bergonzo, ... Journal of Biological Chemistry 294 (48), 18046-18056, 2019 | 12 | 2019 |
| Molecular Modeling of Nucleic Acid Structure: Setup and Analysis R Galindo‐Murillo, C Bergonzo, TE Cheatham Current Protocols in Nucleic Acid Chemistry, 7.10. 1-7.10. 21, 2014 | 11 | 2014 |
| HDX-MS and MD Simulations Provide Evidence for Stabilization of the IgG1—FcγRIa (CD64a) Immune Complex Through Intermolecular Glycoprotein Bonds KW Anderson, C Bergonzo, K Scott, IL Karageorgos, ES Gallagher, ... Journal of molecular biology 434 (2), 167391, 2022 | 10 | 2022 |
| Mg2+ binding promotes SLV as a scaffold in varkud satellite ribozyme SLI-SLV kissing loop junction C Bergonzo, TE Cheatham Biophysical Journal 113 (2), 313-320, 2017 | 10 | 2017 |
| Accuracy of MD solvent models in RNA structure refinement assessed via liquid-crystal NMR and spin relaxation data C Bergonzo, A Grishaev Journal of structural biology 207 (3), 250-259, 2019 | 9 | 2019 |
Thomas E. Cheatham, IIIProfessor of Medicinal Chemistry; Director Research Computing; University of UtahVerified email at utah.edu
