<div dir="ltr">One significant advantage of OpenFold -- beyond its active open-source development, its pytorch implementation (thus being more interoperable with common external ML libraries) -- is its release of training code. So if Odyssey wants to fine-tune predictions on a protein family of particular interest to Odyssey, OpenFold's your answer. (You all can actually join the OpenFold consortium -- which organizes not just OpenFold the existing project but diverse additional open source ML development directions -- for a small annual donation.) <div><br></div><div>In some respects single-sequence models like OmegaFold have advantages -- you don't need a heterogenous compute environment, with a good GPU for inference but a lot of CPU cores for MSA precomputation. It's not a total panacea though; embedding in a large language model is a significant computation.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Sep 22, 2022 at 11:09 AM Chip Lesburg <<a href="mailto:chip@odysseytx.com">chip@odysseytx.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg-5668487297796317354">
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<p class="MsoNormal">Hi PHENIX users,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">At this past summer’s <a href="https://www.grc.org/diffraction-methods-in-structural-biology-conference/2022/" target="_blank">
Diffraction Methods GRC meeting</a>, Tom Terwilliger presented the utility of incorporating AlphaFold2 predictions during structure fitting and rebuilding. I wonder if anyone has experience using that or an alternative such as
<a href="https://www.biorxiv.org/content/10.1101/2022.07.21.500999v1" target="_blank">OmegaFold</a> or
<a href="https://github.com/aqlaboratory/openfold" target="_blank">OpenFold</a>? Are any of these easier or harder to get set up?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Chip<u></u><u></u></p>
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<td style="width:300px;color:rgb(60,60,59);padding-left:10px;border-left:1px solid rgb(198,198,197)" valign="top"><span style="font-family:"Montserrat Light";font-size:8pt"><span style="font-size:11pt;font-family:"Montserrat Light""><span style="color:rgb(0,0,0);font-family:"Montserrat Light""><span style="font-size:13pt"><span style="color:rgb(0,45,106)">Charles Lesburg</span></span><span style="color:rgb(0,45,106)"> </span></span><strong style="color:rgb(0,0,0);font-family:"Montserrat Light""><span style="color:rgb(0,45,106)"> </span> <br></strong></span>
</span><span style="font-family:Montserrat;font-size:8pt"><span style="font-size:9pt"><span style="font-size:10pt"><span style="font-family:Montserrat;font-size:10pt"><span style="font-size:9pt"><b style="color:rgb(0,45,106)">Vice President, Structural Biology<br></b></span></span>
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