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faq.html
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<!DOCTYPE HTML>
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<h2>Frequently Asked Questions</h2>
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<h3>Data Analysis</h3>
<h4>What pulse sequences are implemented in TITAN?</h4>
<p>The following pulse sequences are implemented in TITAN: HSQC, HMQC, HZQC/HDQC, gHMQC, CPMG-HSQC, CPMG-gHMQC, COSY, and NOESY pulse sequences.</p>
<p>However, to the extent that relaxation or chemical exchange during magnetization transfer steps can be neglected, other experiments such as transverse relaxation-optimized spectroscopy (TROSY)
and sensitivity-enhanced HSQCs may still be analyzed as if acquired with a regular HSQC pulse sequence, but the user should be aware of the additional assumptions involved in such an analysis.</p>
<h4>What is the optimal shape and selection of a ROI?</h4>
<p> ROIs should extend approximately two to three linewidths from the center of resonances and contain the entire region of the spectrum within
which resonances are observed across the titration.</p>
<p>Overly large ROIs will result in increased noise, slower fitting calculations, and potentially inadvertant overlaps with
adjacent resonances. Conversely, tightly cropped ROIs will reduce the accuracy of fitted linewidths.</p>
<hr />
<h3>Data Acquisition</h3>
<h4>What should the concentrations of my samples be?</h4>
<p> Optimal results are obtained when the protein concentration is comparable to K<sub>d</sub>. Protein concentrations of at least 10 μM are
required, but higher protein concentrations, around 50-100μ M, will generally allow sufficiently high signal-to-noise ratios to be obtained in
less than an hour. The final ligand concentration should be sufficient to fully saturate the binding: the greater of at least three times the Kd or
two equivalents relative to the protein concentration.</p>
<h4>How many titration points should be acquired?</h4>
<p> Approximately 8-12 titration points should be acquired. However, these guidelines are based on a simple 1:1 association reaction, P + L ⇌ PL.
The identification and analysis of more complex binding mechanisms may benefit from a greater number of points or, for example,
varying the protein concentration in addition to that of the ligand.</p>
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Launch the TITAN app!
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<h3>How to Run the TITAN app from within MATLAB</h3>
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Start the main TITAN graphical user interface with the command 'TITAN'.
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Please <a href="contact.html">contact</a> Chris Waudby in case of problems downloading, installing, or running TITAN.
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