J
John Chodera
Researcher at California Institute for Quantitative Biosciences
Publications - 12
Citations - 446
John Chodera is an academic researcher from California Institute for Quantitative Biosciences. The author has contributed to research in topics: Collective behavior & Force spectroscopy. The author has an hindex of 6, co-authored 12 publications receiving 389 citations.
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Journal ArticleDOI
On the Use of Experimental Observations to Bias Simulated Ensembles.
Jed W. Pitera,John Chodera +1 more
TL;DR: It is shown how the maximum entropy formalism provides a principled approach to enforce concordance with experimental measurements in a minimally biased way, yielding restraints that are linear functions of the target observables and specifying a straightforward scheme to determine the biasing weights.
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Systematic errors in isothermal titration calorimetry: Concentrations and baselines
Joel Tellinghuisen,John Chodera +1 more
TL;DR: In the study of 1:1 binding by isothermal titration calorimetry, reagent concentration errors are fully absorbed in the data analysis, giving incorrect values for the key parameters with no effect on the least-squares statistics.
Journal ArticleDOI
Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments.
John Chodera,Vijay S. Pande +1 more
TL;DR: Comparison of the observed splitting probability with that computed from the kinetic model provides a simple test to reject poor reaction coordinates for a force spectroscopy measurement of a DNA hairpin.
Journal ArticleDOI
Limitations of Constant-Force-Feedback Experiments
Phillip J. Elms,Phillip J. Elms,John Chodera,Carlos Bustamante,Susan Marqusee,Susan Marqusee +5 more
TL;DR: It is demonstrated that the commonly used technique of force feedback has severe limitations when used to evaluate rapid macromolecular conformational transitions, and the causes are elucidated and a simple test is provided to identify and evaluate the magnitude of the effect.
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The Mechanical Properties of PCNA: Implications for the Loading and Function of a DNA Sliding Clamp
TL;DR: A coarse-grained elastic model was built; its strong correspondence to the all-atom MD simulations of PCNA suggests that the behavior of the open clamp is primarily due to elastic deformation governed by the topology of the clamp domains.