Augmenting the anisotropic network model with torsional potentials improves PATH performance, enabling detailed comparison with experimental rate data

Srinivas Niranj Chandrasekaran, Charles W. Carter

Research output: Contribution to journalArticle

  • 3 Citations

Abstract

PATH algorithms for identifying conformational transition states provide computational parameters-time to the transition state, conformational free energy differences, and transition state activation energies-for comparison to experimental data and can be carried out sufficiently rapidly to use in the "high throughput" mode.These advantages are especially useful for interpreting results from combinatorial mutagenesis experiments. This report updates the previously published algorithm with enhancements that improve correlations between PATH convergence parameters derived from virtual variant structures generated by RosettaBackrub and previously published kinetic data for a complete, four-way combinatorial mutagenesis of a conformational switch in Tryptophanyl-tRNA synthetase.

LanguageEnglish (US)
Article number032103
JournalStructural Dynamics
Volume4
Issue number3
DOIs
StatePublished - May 1 2017

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Mutagenesis
mutagenesis
Tryptophan-tRNA Ligase
Free energy
Activation energy
Switches
Throughput
Kinetics
switches
free energy
activation energy
augmentation
Experiments
kinetics
Transfer RNA

ASJC Scopus subject areas

  • Radiation
  • Instrumentation
  • Condensed Matter Physics
  • Spectroscopy

Cite this

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