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Paul C. Whitford
Researcher at Northeastern University
Publications - 95
Citations - 4107
Paul C. Whitford is an academic researcher from Northeastern University. The author has contributed to research in topics: Energy landscape & Transfer RNA. The author has an hindex of 31, co-authored 82 publications receiving 3524 citations. Previous affiliations of Paul C. Whitford include Los Alamos National Laboratory & Rice University.
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An all‐atom structure‐based potential for proteins: Bridging minimal models with all‐atom empirical forcefields
Paul C. Whitford,Jeffrey K. Noel,Shachi Gosavi,Alexander Schug,Kevin Y. Sanbonmatsu,José N. Onuchic +5 more
TL;DR: The robustness of folding mechanisms are robust to variations of the energetic parameters, and the global folding mechanisms in a Cα model and the all‐atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model.
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Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites
Andreas H. Ratje,Andreas H. Ratje,Justus Loerke,Aleksandra Mikolajka,Matthias Brünner,Peter W. Hildebrand,Agata L. Starosta,Alexandra Dönhöfer,Sean R. Connell,Paola Fucini,Thorsten Mielke,Paul C. Whitford,José N. Onuchic,Yanan Yu,Karissa Y. Sanbonmatsu,Roland K. Hartmann,Pawel A. Penczek,Daniel N. Wilson,Christian M. T. Spahn +18 more
TL;DR: Cryoelectron microscopy analysis is used to resolve two previously unseen subpopulations within Thermus thermophilus EF-G–ribosome complexes at subnanometre resolution and provides direct structural and mechanistic insight into the ‘missing link’ in terms of tRNA intermediates involved in the universally conserved translocation process.
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SMOG@ctbp: simplified deployment of structure-based models in GROMACS.
TL;DR: A web tool user is able to upload any multi-chain biomolecular system consisting of standard RNA, DNA and amino acids in PDB format and receive as output all files necessary to implement the model in GROMACS.
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Conformational transitions of adenylate kinase: switching by cracking.
TL;DR: A coarse grained model is employed to explore the interplay between protein structure, folding and function which is applicable to allosteric or non-allosteric proteins and it is demonstrated that local unfolding may be due, in part, to competing intra-protein interactions.
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Nanopore-Based Measurements of Protein Size, Fluctuations, and Conformational Changes
Pradeep Waduge,Rui Hu,Prasad Bandarkar,Hirohito Yamazaki,Benjamin Cressiot,Qing Zhao,Paul C. Whitford,Meni Wanunu +7 more
TL;DR: The measurements reveal a correlation between the mean current blockade amplitude and the radius of gyration for each protein, and the magnitude of the structural fluctuations, as probed by experiments and simulations, correlates with the ratio of α-helix to β-sheet content.