| An all‐atom structure‐based potential for proteins: bridging minimal models with all‐atom empirical forcefields PC Whitford, JK Noel, S Gosavi, A Schug, KY Sanbonmatsu, JN Onuchic Proteins: Structure, Function, and Bioinformatics 75 (2), 430-441, 2009 | 398 | 2009 |
| Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites AH Ratje, J Loerke, A Mikolajka, M Brünner, PW Hildebrand, AL Starosta, ... Nature 468 (7324), 713-716, 2010 | 393 | 2010 |
| SMOG@ ctbp: simplified deployment of structure-based models in GROMACS JK Noel, PC Whitford, KY Sanbonmatsu, JN Onuchic Nucleic acids research 38 (suppl_2), W657-W661, 2010 | 344 | 2010 |
| Conformational transitions of adenylate kinase: switching by cracking PC Whitford, O Miyashita, Y Levy, JN Onuchic Journal of molecular biology 366 (5), 1661-1671, 2007 | 338 | 2007 |
| Nanopore-based measurements of protein size, fluctuations, and conformational changes P Waduge, R Hu, P Bandarkar, H Yamazaki, B Cressiot, Q Zhao, ... ACS nano 11 (6), 5706-5716, 2017 | 267 | 2017 |
| SMOG 2: a versatile software package for generating structure-based models JK Noel, M Levi, M Raghunathan, H Lammert, RL Hayes, JN Onuchic, ... PLoS computational biology 12 (3), e1004794, 2016 | 257 | 2016 |
| The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function JK Noel, PC Whitford, JN Onuchic The Journal of Physical Chemistry B 116 (29), 8692-8702, 2012 | 227 | 2012 |
| Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways PC Whitford, P Geggier, RB Altman, SC Blanchard, JN Onuchic, ... Rna 16 (6), 1196-1204, 2010 | 213 | 2010 |
| Biomolecular dynamics: order-disorder transitions and energy landscapes PC Whitford, KY Sanbonmatsu, JN Onuchic Reports on Progress in Physics 75 (7), 076601, 2012 | 133 | 2012 |
| Conformational transitions in adenylate kinase: allosteric communication reduces misligation PC Whitford, S Gosavi, JN Onuchic Journal of Biological Chemistry 283 (4), 2042-2048, 2008 | 126 | 2008 |
| Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function PC Whitford, A Schug, J Saunders, SP Hennelly, JN Onuchic, ... Biophysical journal 96 (2), L7-L9, 2009 | 112 | 2009 |
| Excited states of ribosome translocation revealed through integrative molecular modeling PC Whitford, A Ahmed, Y Yu, SP Hennelly, F Tama, CMT Spahn, ... Proceedings of the National Academy of Sciences 108 (47), 18943-18948, 2011 | 101 | 2011 |
| Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch RL Hayes, JK Noel, U Mohanty, PC Whitford, SP Hennelly, JN Onuchic, ... Journal of the American Chemical Society 134 (29), 12043-12053, 2012 | 96 | 2012 |
| Connecting the kinetics and energy landscape of tRNA translocation on the ribosome PC Whitford, SC Blanchard, JHD Cate, KY Sanbonmatsu PLoS computational biology 9 (3), e1003003, 2013 | 95 | 2013 |
| Extracting function from a β-trefoil folding motif S Gosavi, PC Whitford, PA Jennings, JN Onuchic Proceedings of the National Academy of Sciences 105 (30), 10384-10389, 2008 | 90 | 2008 |
| Mutations as trapdoors to two competing native conformations of the Rop-dimer A Schug, PC Whitford, Y Levy, JN Onuchic Proceedings of the National Academy of Sciences 104 (45), 17674-17679, 2007 | 80 | 2007 |
| How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome JK Noel, PC Whitford Nature communications 7 (1), 13314, 2016 | 71 | 2016 |
| Energy landscape along an enzymatic reaction trajectory: hinges or cracks? PC Whitford, JN Onuchic, PG Wolynes Taylor & Francis Group 2 (2), 61-64, 2008 | 70 | 2008 |
| Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding J Wang, RJ Oliveira, X Chu, PC Whitford, J Chahine, W Han, E Wang, ... Proceedings of the National Academy of Sciences 109 (39), 15763-15768, 2012 | 69 | 2012 |
| Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome PC Whitford, JN Onuchic, KY Sanbonmatsu Journal of the American Chemical Society 132 (38), 13170-13171, 2010 | 66 | 2010 |
