| Year |
Citation |
Score |
| 2023 |
Byju S, Hassan A, Whitford PC. The energy landscape of the ribosome. Biopolymers. e23570. PMID 38051695 DOI: 10.1002/bip.23570 |
0.316 |
|
| 2023 |
Morcos F, Whitford PC, Cheung MS. Biography of José N. Onuchic. The Journal of Physical Chemistry. B. 127: 7556-7557. PMID 37674460 DOI: 10.1021/acs.jpcb.3c05233 |
0.42 |
|
| 2023 |
Morcos F, Whitford PC, Cheung MS. Tribute to José N. Onuchic. The Journal of Physical Chemistry. B. 127: 7553-7555. PMID 37674459 DOI: 10.1021/acs.jpcb.3c05234 |
0.419 |
|
| 2023 |
Singh V, Itoh Y, Del'Olio S, Hassan A, Naschberger A, Flygaard RK, Nobe Y, Izumikawa K, Aibara S, Andréll J, Whitford PC, Barrientos A, Taoka M, Amunts A. Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications. Biorxiv : the Preprint Server For Biology. PMID 37503168 DOI: 10.1101/2023.05.24.542018 |
0.346 |
|
| 2022 |
Hassan A, Byju S, Freitas FC, Roc C, Pender N, Nguyen K, Kimbrough EM, Mattingly JM, Gonzalez RL, de Oliveira RJ, Dunham CM, Whitford PC. Ratchet, swivel, tilt and roll: a complete description of subunit rotation in the ribosome. Nucleic Acids Research. PMID 36583339 DOI: 10.1093/nar/gkac1211 |
0.795 |
|
| 2022 |
Dias RVR, Ferreira CTA, Jennings PA, Whitford PC, Oliveira LC. Csk αC Helix: A Computational Analysis of an Essential Region for Conformational Transitions. The Journal of Physical Chemistry. B. 126: 10587-10596. PMID 36512419 DOI: 10.1021/acs.jpcb.2c05408 |
0.322 |
|
| 2022 |
Wang Y, Wang A, Mohanty U, Whitford PC. Precise Steric Features Control Aminoacyl-tRNA Accommodation on the Ribosome. The Journal of Physical Chemistry. B. 126: 8447-8459. PMID 36251478 DOI: 10.1021/acs.jpcb.2c05513 |
0.365 |
|
| 2022 |
Wang A, Levi M, Mohanty U, Whitford PC. Diffuse Ions Coordinate Dynamics in a Ribonucleoprotein Assembly. Journal of the American Chemical Society. 144: 9510-9522. PMID 35593477 DOI: 10.1021/jacs.2c04082 |
0.307 |
|
| 2022 |
Markosian C, Staquicini DI, Dogra P, Dodero-Rojas E, Lubin JH, Tang FHF, Smith TL, Contessoto VG, Libutti SK, Wang Z, Cristini V, Khare SD, Whitford PC, Burley SK, Onuchic JN, et al. Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection. Molecular Biology and Evolution. PMID 35511693 DOI: 10.1093/molbev/msac091 |
0.445 |
|
| 2021 |
Freitas FC, Fuchs G, de Oliveira RJ, Whitford PC. The dynamics of subunit rotation in a eukaryotic ribosome. Biophysica. 1: 204-221. PMID 37484008 DOI: 10.3390/biophysica1020016 |
0.401 |
|
| 2021 |
Hassan A, Byju S, Whitford PC. The energetics of subunit rotation in the ribosome. Biophysical Reviews. 13: 1029-1037. PMID 35059025 DOI: 10.1007/s12551-021-00877-8 |
0.39 |
|
| 2021 |
Markosian C, Staquicini DI, Dogra P, Dodero-Rojas E, Tang FHF, Smith TL, Contessoto VG, Libutti SK, Wang Z, Cristini V, Whitford PC, Burley SK, Onuchic JN, Pasqualini R, Arap W. Apropos of Universal Epitope Discovery for COVID-19 Vaccines: A Framework for Targeted Phage Display-Based Delivery and Integration of New Evaluation Tools. Biorxiv : the Preprint Server For Biology. PMID 34676381 DOI: 10.1101/2021.08.30.458222 |
0.388 |
|
| 2021 |
de Oliveira AB, Contessoto VG, Hassan A, Byju S, Wang A, Wang Y, Dodero-Rojas E, Mohanty U, Noel JK, Onuchic JN, Whitford PC. SMOG 2 and OpenSMOG: Extending the limits of structure-based models. Protein Science : a Publication of the Protein Society. PMID 34655449 DOI: 10.1002/pro.4209 |
0.728 |
|
| 2021 |
Dodero-Rojas E, Onuchic JN, Whitford PC. Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. Elife. 10. PMID 34463614 DOI: 10.7554/eLife.70362 |
0.506 |
|
| 2021 |
Staquicini DI, Tang FHF, Markosian C, Yao VJ, Staquicini FI, Dodero-Rojas E, Contessoto VG, Davis D, O'Brien P, Habib N, Smith TL, Bruiners N, Sidman RL, Gennaro ML, Lattime EC, ... ... Whitford PC, et al. Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34234013 DOI: 10.1073/pnas.2105739118 |
0.404 |
|
| 2021 |
Staquicini DI, Tang FHF, Markosian C, Yao VJ, Staquicini FI, Dodero-Rojas E, Contessoto VG, Davis D, O'Brien P, Habib N, Smith TL, Bruiners N, Sidman RL, Gennaro ML, Lattime EC, ... ... Whitford PC, et al. Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain. Biorxiv : the Preprint Server For Biology. PMID 33758865 DOI: 10.1101/2021.03.15.435496 |
0.408 |
|
| 2020 |
Levi M, Walak K, Wang A, Mohanty U, Whitford PC. A steric gate controls P/E hybrid-state formation of tRNA on the ribosome. Nature Communications. 11: 5706. PMID 33177497 DOI: 10.1038/s41467-020-19450-0 |
0.376 |
|
| 2020 |
Whitford PC, Jiang W, Serwer P. Simulations of Phage T7 Capsid Expansion Reveal the Role of Molecular Sterics on Dynamics. Viruses. 12. PMID 33171826 DOI: 10.3390/v12111273 |
0.361 |
|
| 2020 |
Bandarkar P, Yang H, Henley RY, Wanunu M, Whitford PC. How Nanopore Translocation Experiments Can Measure RNA Unfolding. Biophysical Journal. PMID 32075749 DOI: 10.1016/J.Bpj.2020.01.030 |
0.485 |
|
| 2020 |
Hassan AH, Whitford PC. Using Simulations to Identify Precise Single-Molecule Probes for Ribosome Dynamics Biophysical Journal. 118: 548a. DOI: 10.1016/J.Bpj.2019.11.2996 |
0.376 |
|
| 2020 |
Levi M, Noel J, Yang H, Kien Nguyen T, Hassan AH, Walak KN, Perrier J, Dukaye L, Horne R, Whitford PC. Precisely Quantifying the Energetics of the Ribosome Biophysical Journal. 118: 181a. DOI: 10.1016/J.Bpj.2019.11.1107 |
0.65 |
|
| 2019 |
Oliveira Junior AB, Yang H, Whitford PC, Leite VBP. Distinguishing biomolecular pathways and metastable states. Journal of Chemical Theory and Computation. PMID 31618581 DOI: 10.1021/Acs.Jctc.9B00704 |
0.425 |
|
| 2019 |
Freitas FC, Lima AN, Contessoto VG, Whitford PC, Oliveira RJ. Drift-diffusion (DrDiff) framework determines kinetics and thermodynamics of two-state folding trajectory and tunes diffusion models. The Journal of Chemical Physics. 151: 114106. PMID 31542001 DOI: 10.1063/1.5113499 |
0.79 |
|
| 2019 |
Yang H, Bandarkar P, Horne R, Leite VBP, Chahine J, Whitford PC. Diffusion of tRNA inside the ribosome is position-dependent. The Journal of Chemical Physics. 151: 085102. PMID 31470725 DOI: 10.1063/1.5113814 |
0.433 |
|
| 2019 |
Levi M, Bandarkar P, Yang H, Wang A, Mohanty U, Noel JK, Whitford PC. Using SMOG 2 to Simulate Complex Biomolecular Assemblies. Methods in Molecular Biology (Clifton, N.J.). 2022: 129-151. PMID 31396902 DOI: 10.1007/978-1-4939-9608-7_6 |
0.711 |
|
| 2019 |
Ermolenko DN, Whitford PC. Experimental and computational techniques for studying structural dynamics and function of RNA. Methods (San Diego, Calif.). PMID 31229650 DOI: 10.1016/J.Ymeth.2019.06.020 |
0.404 |
|
| 2019 |
Levi M, Noel JK, Whitford PC. Studying ribosome dynamics with simplified models. Methods (San Diego, Calif.). PMID 30935976 DOI: 10.1016/J.Ymeth.2019.03.023 |
0.694 |
|
| 2019 |
Levi M, Whitford PC. Dissecting the Energetics of Subunit Rotation in the Ribosome. The Journal of Physical Chemistry. B. PMID 30844276 DOI: 10.1021/Acs.Jpcb.9B00178 |
0.473 |
|
| 2018 |
Yang H, Perrier J, Whitford PC. Disorder guides domain rearrangement in EF-Tu. Proteins. PMID 30035820 DOI: 10.1002/Prot.25575 |
0.423 |
|
| 2018 |
Yang H, Noel J, Whitford PC. Anisotropic Fluctuations in the Ribosome Determine aa-tRNA Kinetics Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.2186 |
0.655 |
|
| 2017 |
Levi M, Nguyen K, Dukaye L, Whitford PC. Quantifying the Relationship between Single-Molecule Probes and Subunit Rotation in the Ribosome. Biophysical Journal. 113: 2777-2786. PMID 29262370 DOI: 10.1016/J.Bpj.2017.10.021 |
0.383 |
|
| 2017 |
Yang H, Noel JK, Whitford PC. Anisotropic Fluctuations in the Ribosome Determine tRNA Kinetics. The Journal of Physical Chemistry. B. PMID 28910101 DOI: 10.1021/Acs.Jpcb.7B06828 |
0.705 |
|
| 2017 |
Waduge P, Hu R, Bandrakar P, Yamazaki H, Cressiot B, Zhao Q, Whitford P, Wanunu M. Nanopore-Based Measurements of Protein Size, Fluctuations, and Conformational Changes. Acs Nano. PMID 28471644 DOI: 10.1021/Acsnano.7B01212 |
0.408 |
|
| 2017 |
Nguyen K, Whitford PC. Challenges in describing ribosome dynamics. Physical Biology. 14: 023001. PMID 28328543 DOI: 10.1088/1478-3975/Aa626B |
0.449 |
|
| 2017 |
Nguyen K, Yang H, Whitford PC. How the Ribosomal A-Site Finger Can Lead to tRNA Species-Dependent Dynamics. The Journal of Physical Chemistry. B. PMID 28276690 DOI: 10.1021/Acs.Jpcb.7B01072 |
0.429 |
|
| 2017 |
Yang H, Whitford PC. The Role of L11 Stalk Fluctuations in aa-tRNA Accommodation Biophysical Journal. 112: 68a. DOI: 10.1016/J.Bpj.2016.11.406 |
0.41 |
|
| 2017 |
Waduge P, Hu R, Bandarkar P, Cressiot B, Whitford P, Wanunu M. Ergodicity Measurements in Native Protein Ensembles using Solid-State Nanopores Biophysical Journal. 112: 190a. DOI: 10.1016/J.Bpj.2016.11.1054 |
0.396 |
|
| 2016 |
Noel JK, Whitford PC. How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome. Nature Communications. 7: 13314. PMID 27796304 DOI: 10.1038/Ncomms13314 |
0.712 |
|
| 2016 |
Nguyen K, Whitford PC. Capturing Transition States for tRNA Hybrid-State Formation in the Ribosome. The Journal of Physical Chemistry. B. PMID 27479146 DOI: 10.1021/Acs.Jpcb.6B04476 |
0.442 |
|
| 2016 |
Noel JK, Levi M, Raghunathan M, Lammert H, Hayes RL, Onuchic JN, Whitford PC. SMOG 2: A Versatile Software Package for Generating Structure-Based Models. Plos Computational Biology. 12: e1004794. PMID 26963394 DOI: 10.1371/Journal.Pcbi.1004794 |
0.772 |
|
| 2016 |
Nguyen K, Whitford PC. Steric interactions lead to collective tilting motion in the ribosome during mRNA-tRNA translocation. Nature Communications. 7: 10586. PMID 26838673 DOI: 10.1038/Ncomms10586 |
0.429 |
|
| 2016 |
Bandarkar P, Yang H, Wanunu M, Whitford P. Characterizing the Structural and Energetic Properties of tRNA during Translocation through a Nanopore Biophysical Journal. 110: 408a. DOI: 10.1016/J.Bpj.2015.11.2203 |
0.447 |
|
| 2016 |
Whitford PC. Quantifying the Energy Landscape of Ribosome Function Biophysical Journal. 110: 352a. DOI: 10.1016/J.Bpj.2015.11.1898 |
0.502 |
|
| 2016 |
Nguyen K, Whitford PC. Simulating mRNA-tRNA Translocation through the Ribosome Biophysical Journal. 110: 234a. DOI: 10.1016/J.Bpj.2015.11.1290 |
0.513 |
|
| 2015 |
Whitford PC. The ribosome's energy landscape: Recent insights from computation. Biophysical Reviews. 7: 301-310. PMID 28510226 DOI: 10.1007/s12551-014-0155-1 |
0.362 |
|
| 2015 |
Hayes RL, Noel JK, Mandic A, Whitford PC, Sanbonmatsu KY, Mohanty U, Onuchic JN. Generalized Manning Condensation Model Captures the RNA Ion Atmosphere. Physical Review Letters. 114: 258105. PMID 26197147 DOI: 10.1103/Physrevlett.114.258105 |
0.792 |
|
| 2015 |
Whitford PC. 69 Quantifying the energy landscapes of ribosome function through simulation. Journal of Biomolecular Structure & Dynamics. 33: 45. PMID 26103280 DOI: 10.1080/07391102.2015.1032686 |
0.386 |
|
| 2015 |
Jackson J, Nguyen K, Whitford PC. Exploring the balance between folding and functional dynamics in proteins and RNA. International Journal of Molecular Sciences. 16: 6868-89. PMID 25822873 DOI: 10.3390/Ijms16046868 |
0.491 |
|
| 2015 |
Whitford PC, Onuchic JN. What protein folding teaches us about biological function and molecular machines. Current Opinion in Structural Biology. 30: 57-62. PMID 25559307 DOI: 10.1016/J.Sbi.2014.12.003 |
0.606 |
|
| 2015 |
Hayes RL, Noel JK, Mandic A, Whitford PC, Sanbonmatsu KY, Mohanty U, Onuchic JN. Generalized Manning Condensation Model Captures the RNA Ion Atmosphere Physical Review Letters. 114. DOI: 10.1103/PhysRevLett.114.258105 |
0.757 |
|
| 2015 |
Nguyen K, Whitford PC. Simulating Ribosome Dynamics and tRNA Translocation Biophysical Journal. 108: 390a-391a. DOI: 10.1016/J.Bpj.2014.11.2140 |
0.517 |
|
| 2015 |
Hayes RL, Noel JK, Mandic A, Whitford PC, Sanbonmatsu KY, Mohanty U, Onuchic JN. Magnesium Dependence of the RNA Free Energy Landscape Biophysical Journal. 108: 235a. DOI: 10.1016/J.Bpj.2014.11.1301 |
0.805 |
|
| 2015 |
Whitford PC. The ribosome’s energy landscape: Recent insights from computation Biophysical Reviews. 7: 301-310. DOI: 10.1007/S12551-014-0155-1 |
0.461 |
|
| 2014 |
Noel JK, Chahine J, Leite VB, Whitford PC. Capturing transition paths and transition states for conformational rearrangements in the ribosome. Biophysical Journal. 107: 2881-90. PMID 25517153 DOI: 10.1016/J.Bpj.2014.10.022 |
0.816 |
|
| 2014 |
Lin X, Eddy NR, Noel JK, Whitford PC, Wang Q, Ma J, Onuchic JN. Order and disorder control the functional rearrangement of influenza hemagglutinin. Proceedings of the National Academy of Sciences of the United States of America. 111: 12049-54. PMID 25082896 DOI: 10.1073/Pnas.1412849111 |
0.792 |
|
| 2014 |
Hayes RL, Noel JK, Whitford PC, Mohanty U, Sanbonmatsu KY, Onuchic JN. Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches. Biophysical Journal. 106: 1508-19. PMID 24703312 DOI: 10.1016/J.Bpj.2014.01.042 |
0.797 |
|
| 2014 |
Noel JK, Leite VB, Chahine J, Whitford PC. Probing Diffusive and Energetic Aspects of Ribosome Function Biophysical Journal. 106: 609a. DOI: 10.1016/J.Bpj.2013.11.3369 |
0.825 |
|
| 2014 |
Noel JK, Whitford P. Excluded Volume of EF-Tu Greatly Reduces the Barrier to Accommodation for aa-tRNA in the Ribosome Biophysical Journal. 106: 490a. DOI: 10.1016/J.Bpj.2013.11.2739 |
0.718 |
|
| 2014 |
Noel JK, Whitford PC. How simulations reveal dynamics, disorder, and the energy landscapes of biomolecular function Israel Journal of Chemistry. DOI: 10.1002/Ijch.201400018 |
0.695 |
|
| 2013 |
Whitford PC, Sanbonmatsu KY. Simulating movement of tRNA through the ribosome during hybrid-state formation. The Journal of Chemical Physics. 139: 121919. PMID 24089731 DOI: 10.1063/1.4817212 |
0.728 |
|
| 2013 |
Whitford PC. Disorder guides protein function. Proceedings of the National Academy of Sciences of the United States of America. 110: 7114-5. PMID 23610426 DOI: 10.1073/Pnas.1305236110 |
0.401 |
|
| 2013 |
Whitford PC, Blanchard SC, Cate JH, Sanbonmatsu KY. Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. Plos Computational Biology. 9: e1003003. PMID 23555233 DOI: 10.1371/Journal.Pcbi.1003003 |
0.689 |
|
| 2013 |
Noel JK, Sanbonmatsu KY, Whitford PC. 35 The energy landscapes of ribosome function Journal of Biomolecular Structure and Dynamics. 31: 21-22. DOI: 10.1080/07391102.2013.786468 |
0.797 |
|
| 2012 |
Jamros MA, Oliveira LC, Whitford PC, Onuchic JN, Adams JA, Jennings PA. Substrate-specific reorganization of the conformational ensemble of CSK implicates novel modes of kinase function. Plos Computational Biology. 8: e1002695. PMID 23028292 DOI: 10.1371/Journal.Pcbi.1002695 |
0.514 |
|
| 2012 |
Wang J, Oliveira RJ, Chu X, Whitford PC, Chahine J, Han W, Wang E, Onuchic JN, Leite VB. Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 109: 15763-8. PMID 23019359 DOI: 10.1073/Pnas.1212842109 |
0.796 |
|
| 2012 |
Whitford PC, Sanbonmatsu KY, Onuchic JN. Biomolecular dynamics: order-disorder transitions and energy landscapes. Reports On Progress in Physics. Physical Society (Great Britain). 75: 076601. PMID 22790780 DOI: 10.1088/0034-4885/75/7/076601 |
0.726 |
|
| 2012 |
Hayes RL, Noel JK, Mohanty U, Whitford PC, Hennelly SP, Onuchic JN, Sanbonmatsu KY. Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch. Journal of the American Chemical Society. 134: 12043-53. PMID 22612276 DOI: 10.1021/Ja301454U |
0.785 |
|
| 2012 |
Noel JK, Whitford PC, Onuchic JN. The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function. The Journal of Physical Chemistry. B. 116: 8692-702. PMID 22536820 DOI: 10.1021/Jp300852D |
0.743 |
|
| 2012 |
Singh JP, Whitford PC, Hayre NR, Onuchic J, Cox DL. Massive conformation change in the prion protein: Using dual-basin structure-based models to find misfolding pathways. Proteins. 80: 1299-307. PMID 22274922 DOI: 10.1002/Prot.24026 |
0.589 |
|
| 2012 |
Ahmed A, Whitford PC, Sanbonmatsu KY, Tama F. Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. Journal of Structural Biology. 177: 561-70. PMID 22019767 DOI: 10.1016/J.Jsb.2011.10.002 |
0.646 |
|
| 2012 |
Whitford PC, Sanbonmatsu K. Probing the Energy Landscape of Ribosome Function Through Simulation Biophysical Journal. 102: 39a. DOI: 10.1016/J.Bpj.2011.11.242 |
0.73 |
|
| 2012 |
Sanbonmatsu KY, Blanchard SC, Whitford PC. Dynamics of very large systems: The ribosome Comprehensive Biophysics. 9: 76-85. DOI: 10.1016/B978-0-12-374920-8.00907-3 |
0.567 |
|
| 2011 |
Whitford PC, Ahmed A, Yu Y, Hennelly SP, Tama F, Spahn CM, Onuchic JN, Sanbonmatsu KY. Excited states of ribosome translocation revealed through integrative molecular modeling. Proceedings of the National Academy of Sciences of the United States of America. 108: 18943-8. PMID 22080606 DOI: 10.1073/Pnas.1108363108 |
0.811 |
|
| 2011 |
Nechushtai R, Lammert H, Michaeli D, Eisenberg-Domovich Y, Zuris JA, Luca MA, Capraro DT, Fish A, Shimshon O, Roy M, Schug A, Whitford PC, Livnah O, Onuchic JN, Jennings PA. Allostery in the ferredoxin protein motif does not involve a conformational switch. Proceedings of the National Academy of Sciences of the United States of America. 108: 2240-5. PMID 21266547 DOI: 10.1073/Pnas.1019502108 |
0.569 |
|
| 2011 |
Whitford PC, Spahn CM, Blanchard SC, Onuchic JN, Sanbonmatsu KY. Revealing the Energy Landscapes of Ribosome Function Biophysical Journal. 100: 238a. DOI: 10.1016/J.Bpj.2010.12.1517 |
0.765 |
|
| 2010 |
Ratje AH, Loerke J, Mikolajka A, Brünner M, Hildebrand PW, Starosta AL, Dönhöfer A, Connell SR, Fucini P, Mielke T, Whitford PC, Onuchic JN, Yu Y, Sanbonmatsu KY, Hartmann RK, et al. Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature. 468: 713-6. PMID 21124459 DOI: 10.1038/Nature09547 |
0.699 |
|
| 2010 |
Whitford PC, Onuchic JN, Sanbonmatsu KY. Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome. Journal of the American Chemical Society. 132: 13170-1. PMID 20806913 DOI: 10.1021/Ja1061399 |
0.711 |
|
| 2010 |
Jamros MA, Oliveira LC, Whitford PC, Onuchic JN, Adams JA, Blumenthal DK, Jennings PA. Proteins at work: a combined small angle X-RAY scattering and theoretical determination of the multiple structures involved on the protein kinase functional landscape. The Journal of Biological Chemistry. 285: 36121-8. PMID 20801888 DOI: 10.1074/Jbc.M110.116947 |
0.578 |
|
| 2010 |
Oliveira RJ, Whitford PC, Chahine J, Wang J, Onuchic JN, Leite VB. The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding. Biophysical Journal. 99: 600-8. PMID 20643080 DOI: 10.1016/J.Bpj.2010.04.041 |
0.799 |
|
| 2010 |
Noel JK, Whitford PC, Sanbonmatsu KY, Onuchic JN. SMOG@ctbp: simplified deployment of structure-based models in GROMACS. Nucleic Acids Research. 38: W657-61. PMID 20525782 DOI: 10.1093/Nar/Gkq498 |
0.822 |
|
| 2010 |
Oliveira RJ, Whitford PC, Chahine J, Leite VB, Wang J. Coordinate and time-dependent diffusion dynamics in protein folding. Methods (San Diego, Calif.). 52: 91-8. PMID 20438841 DOI: 10.1016/J.Ymeth.2010.04.016 |
0.781 |
|
| 2010 |
Whitford PC, Geggier P, Altman RB, Blanchard SC, Onuchic JN, Sanbonmatsu KY. Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. Rna (New York, N.Y.). 16: 1196-204. PMID 20427512 DOI: 10.1261/Rna.2035410 |
0.763 |
|
| 2010 |
Singh JP, Cox DL, Whitford PC. Structure-Based Models for Alpha-Helical to Beta-Helical Conformation Change in the C-Terminal of the Mammalian Prion Protein Biophysical Journal. 98: 453a. DOI: 10.1016/J.Bpj.2009.12.2464 |
0.4 |
|
| 2010 |
Whitford PC, Geggier P, Altman R, Blanchard SC, Onuchic JN, Sanbonmatsu KY. Simulations of the Ribosome Suggest Reversible Transitions and Parallel Pathways are Involved in the Large-Scale Functional Motions of tRNA During Translation Biophysical Journal. 98: 259a. DOI: 10.1016/J.Bpj.2009.12.1412 |
0.629 |
|
| 2009 |
Whitford PC, Schug A, Saunders J, Hennelly SP, Onuchic JN, Sanbonmatsu KY. Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function. Biophysical Journal. 96: L7-9. PMID 19167285 DOI: 10.1016/J.Bpj.2008.10.033 |
0.783 |
|
| 2009 |
Whitford PC, Noel JK, Gosavi S, Schug A, Sanbonmatsu KY, Onuchic JN. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields. Proteins. 75: 430-41. PMID 18837035 DOI: 10.1002/Prot.22253 |
0.806 |
|
| 2009 |
Whitford PC, Schug A, Noel JK, Gosavi S, Hennelly SP, Sanbonmatsu KY, Onuchic JN. All-atom Models For RNA And Proteins: Simulating Folding And Function Biophysical Journal. 96: 555a. DOI: 10.1016/J.Bpj.2008.12.3648 |
0.82 |
|
| 2008 |
Whitford PC, Onuchic JN, Wolynes PG. Energy landscape along an enzymatic reaction trajectory: hinges or cracks? Hfsp Journal. 2: 61-4. PMID 19404472 DOI: 10.2976/1.2894846 |
0.569 |
|
| 2008 |
Gosavi S, Whitford PC, Jennings PA, Onuchic JN. Extracting function from a beta-trefoil folding motif. Proceedings of the National Academy of Sciences of the United States of America. 105: 10384-9. PMID 18650393 DOI: 10.1073/Pnas.0801343105 |
0.456 |
|
| 2008 |
Whitford PC, Gosavi S, Onuchic JN. Conformational transitions in adenylate kinase. Allosteric communication reduces misligation. The Journal of Biological Chemistry. 283: 2042-8. PMID 17998210 DOI: 10.1074/Jbc.M707632200 |
0.543 |
|
| 2008 |
Gosavi S, Whitford PC, Jennings PA, Onuchic JN. Extracting function from a β-trefoil folding motif (Proceedings of the National Academy of Sciences of the United States of America (2008) 105, 30 (11384-10389) DOI: 10.1073/pnas.0801343105)) Proceedings of the National Academy of Sciences of the United States of America. 105: 16057. DOI: 10.1073/pnas.0808551105 |
0.399 |
|
| 2008 |
Gosavi S, Whitford PC, Jennings PA, Onuchic JN. Extracting function from a β-trefoil folding motif (Proceedings of the National Academy of Sciences of the United States of America (2008) 105, 30 (11384-10389) DOI: 10.1073/pnas.0801343105)) Proceedings of the National Academy of Sciences of the United States of America. 105: 16057. DOI: 10.1073/pnas.0808551105 |
0.399 |
|
| 2007 |
Schug A, Whitford PC, Levy Y, Onuchic JN. Mutations as trapdoors to two competing native conformations of the Rop-dimer. Proceedings of the National Academy of Sciences of the United States of America. 104: 17674-9. PMID 17968016 DOI: 10.1073/Pnas.0706077104 |
0.578 |
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| 2007 |
Whitford PC, Miyashita O, Levy Y, Onuchic JN. Conformational transitions of adenylate kinase: switching by cracking. Journal of Molecular Biology. 366: 1661-71. PMID 17217965 DOI: 10.1016/J.Jmb.2006.11.085 |
0.587 |
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| 2007 |
Mills JE, Whitford PC, Shaffer J, Onuchic JN, Adams JA, Jennings PA. A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity. Journal of Molecular Biology. 365: 1460-8. PMID 17137590 DOI: 10.1016/J.Jmb.2006.10.076 |
0.49 |
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| Show low-probability matches. |