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<p class="MsoNormal">Hi Tom,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you so much! It is great that I inspired you to write this command.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Since I have you (and I am no expert in structural biology), do you think alphafold will soon update larger proteins? Is there still a limitation? On your Youtube videos you guys state after 700 aa the system crashes a lot.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">If I know a protein that perhaps might have a similar structure to my protein would it help resolves these clashing problems?
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">As you can see I tried to hide what my protein of interest was but it seems there are not a lot of 5005 amino acid proteins =).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you again!<o:p></o:p></p>
<p class="MsoNormal">Yunsik<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b>From:</b> Tom Goddard <goddard@sonic.net> <br>
<b>Sent:</b> Thursday, September 9, 2021 3:17 PM<br>
<b>To:</b> Yunsik Kang <kangy@ohsu.edu><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> [EXTERNAL] AlphaFold model for large proteins<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Yunsik, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Inspired by your question and Tristan Croll's comment that the AlphaFold database has human proteins longer than 1400 amino acids computed as separate 1400 amino acid chunks I made a ChimeraX command "bigalpha" that loads and aligns these
chunks.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a href="https://rbvi.github.io/chimerax-recipes/big_alphafold/bigalpha.html">https://rbvi.github.io/chimerax-recipes/big_alphafold/bigalpha.html</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I attach two images and a PDB model made by running that command in ChimeraX for 5005 amino acid transmembrane protein<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Q2LD37 | K1109_HUMAN Transmembrane protein KIAA1109 OS=Homo sapiens OX=9606 GN=KIAA1109 PE=1 SV=2<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">and also here are a few other examples I looked at yesterday.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a href="https://twitter.com/UCSFChimeraX/status/1435870388043411458">https://twitter.com/UCSFChimeraX/status/1435870388043411458</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a href="https://twitter.com/UCSFChimeraX/status/1435760774824169474">https://twitter.com/UCSFChimeraX/status/1435760774824169474</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a href="https://twitter.com/UCSFChimeraX/status/1435859111053193216">https://twitter.com/UCSFChimeraX/status/1435859111053193216</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Keep in mind that the pieces of these models are not aligned in a reliable way and probably clash badly with each other because AlphaFold did not compute them as part of one structure. So these structures should only give you a very rough
idea about the protein.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Tom<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">This is the confidence coloring determined by AlphaFold, red low, blue high confidence. To reproduce this color using ChimeraX daily build open the PDB model and type command "color bfactor #1 palette alphafold". (The confidence value
is saved as the bfactor in the PDB file).<o:p></o:p></p>
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<p class="MsoNormal"><img border="0" width="1132" height="674" style="width:11.7916in;height:7.0208in" id="_x0000_i1025" src="cid:image001.png@01D7A590.EC640310"><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Different AlphaFold chunks have different colors and chain identifiers in the PDB model.<o:p></o:p></p>
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<p class="MsoNormal"><img border="0" width="1132" height="674" style="width:11.7916in;height:7.0208in" id="_x0000_i1026" src="cid:image002.png@01D7A590.EC640310"><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal">On Sep 8, 2021, at 2:45 PM, Yunsik Kang via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hello,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">My name is Yunsik Kang, and I am a postdoc in Marc Freeman’s lab at the Vollum Institute.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I would love to use ChimeraX to predict the structure of my protein of interest. I watched all the YouTube videos and tried to run the program.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Unfortunately, my protein is 5005 amino acids in humans and 2958 aa in yeast. I get a message “<span style="font-size:10.5pt;font-family:"Courier New";color:#212121;background:white">Please use the full AlphaFold system for long sequences.”</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">My question is what is the best way to approach this problem? Should I cut the protein in half and run the program? In one of the videos, it mentions after 700 aa it will have problems. Will it work if I get Colab-Pro? Or would the server
crash no matter what.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I am not a structural biologist, but I hope the structure can help be predict me with my research. <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Thank you,<o:p></o:p></p>
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<p class="MsoNormal">Yunsik<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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<p class="MsoNormal"><o:p> </o:p></p>
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