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 strategy for a Markov state model (MSM).
The Optimal Probes Software source code is available upon request.
Please contact the Principal Investigator at the following email address:
diwakar [at] illinois [dot] edu
Visit Optimal Probes Wiki for a tutorial and examples.
Mittal S and Shukla D. "Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity". Journal of Physical Chemistry B (2017)
Mittal S and Shukla D. "Optimal Probes: An Efficient Method to Select Deer Distance Restraints using Machine Learning". Biophysical Journal 112.3 (2017).
Selvam B, Mittal S and Shukla D. "In silico Predictions of Conformational States of Bacterial Transporter PepTSo". Submitted (2018)