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<p>To whom it may concern,<br>
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<p><br>
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<p>I have just started working on a project which includes docking and analysis of the results several weeks ago. So figuring out software for docking and the docking procedure itself was one set of problems (solved), and now I could really use your help in
order to analyze my data - docking results (output files).<br>
</p>
<p>At the moment, I am using Windows 10 (x64), Chimera 1.14, AutoDock Vina 1.1.2 and AutoDock 4.2.6.<br>
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<p><br>
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<p><span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);">So, I have a protein (ion-channel) and several different ligands, for which I want
to see how they and if they (at all) may interact with the protein. Therefore I dock the ligand in the two mentioned programs and got different output files. Vina generates a single file with 9 different positions, and 4.2. generates 9 different files for
each position.</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);"><br>
</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);">Now, the first problem I encountered was that in Chimera I can open and analyze only
Vina output (single file). How do I open 4.2. output?</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);"><br>
</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);">The second problem is that I am able (know how) to analyze polar interactions (HBonds).
But can I somehow check for hydrophobic or other kind of interactions?</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);"><br>
</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);">The third thing is that, for example, I have Vina output files for ligand docked
in 2 different (but adjacent) places in protein (so 18 positions in total). Is there any chance to merge those files so I can see the energy differences among all of them?</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);"><br>
</span></p>
<p><font color="#212121" face="Segoe UI, Segoe WP, Segoe UI WPC, Tahoma, Arial, sans-serif"><span style="font-size: 15px;">Fourthly, is there any way to merge vina and an other program's output (4.2 or DOCK for example) and see if there are common structures
(same one generated by both) and the ones that are not common for the two?</span></font></p>
<p><font color="#212121" face="Segoe UI, Segoe WP, Segoe UI WPC, Tahoma, Arial, sans-serif"><span style="font-size: 15px;"><br>
</span></font></p>
<p><font color="#212121" face="Segoe UI, Segoe WP, Segoe UI WPC, Tahoma, Arial, sans-serif"><span style="font-size: 15px;">Finally, is there any graphical way of representing the docking poses and see the likeliness of the binding of a certain poses? Or some
sort of clustering of poses into more probable binding candidates or something similar?</span></font></p>
<p><font color="#212121" face="Segoe UI, Segoe WP, Segoe UI WPC, Tahoma, Arial, sans-serif"><span style="font-size: 15px;"><br>
</span></font></p>
<p><font color="#212121" face="Segoe UI, Segoe WP, Segoe UI WPC, Tahoma, Arial, sans-serif"><span style="font-size: 15px;">Thank you in advance,</span></font></p>
<p><font color="#212121" face="Segoe UI, Segoe WP, Segoe UI WPC, Tahoma, Arial, sans-serif"><span style="font-size: 15px;"><br>
</span></font></p>
<p><font color="#212121" face="Segoe UI, Segoe WP, Segoe UI WPC, Tahoma, Arial, sans-serif"><span style="font-size: 15px;">Denis</span></font></p>
<p><span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);"><br>
</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);"><br>
</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);"><br>
</span></p>
<p><span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);"><br>
</span></p>
<p><br style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);">What kind of docking</span><br style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);">What you want to do, meaning achive</span><br style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);">Which steps have you carried out</span><br style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: "Segoe UI", "Segoe WP", "Segoe UI WPC", Tahoma, Arial, sans-serif; font-size: 15px; background-color: rgb(255, 255, 255);">Description of the status, when you get stuck</span><br>
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