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Optimal Probes is a software package to predict the smallest set of residue pairs for site-directed spin labeling for DEER/EPR experiments that best capture the slowest dynamics in a protein of interest. It uses molecular dynamics (MD) simulation datasets and a hyperparameter optimization strategy¹ for a Markov state model (MSM).

This website explains the workflow and is a guide to the user to obtain their own predictions.

For more information, please visit http://www.shuklagroup.org.

Citation

Mittal, S and Shukla, D. "Optimal Probes: An Efficient Method to Select Deer Distance Restraints using Machine Learning." Biophysical Journal 112.3 (2017).

References

[1] McGibbon, R T, and Pande, V S. "Variational cross-validation of slow dynamical modes in molecular kinetics." The Journal of chemical physics 142.12 (2015).