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.)

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.

On Thu, Sep 22, 2022 at 11:09 AM Chip Lesburg <chip@odysseytx.com> wrote:

Hi PHENIX users,

At this past summer’s Diffraction Methods GRC meeting, 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 OmegaFold or OpenFold? Are any of these easier or harder to get set up?

Chip

Charles Lesburg
Vice President, Structural Biology

M 908-265-2064
301 Binney Street, Cambridge, MA 02142
odysseytx.com

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	Charles Lesburg Vice President, Structural Biology M 908-265-2064 301 Binney Street, Cambridge, MA 02142 odysseytx.com
This message is for the named person's use only. It may contain confidential, proprietary or legally privileged information. If you receive this message in error, please immediately delete it and all copies of it from your system, destroy any hard copies of it and notify the sender. ODYSSEY THERAPEUTICS, INC. ("ODYSSEY THERAPEUTICS") reserves the right to monitor all e-mail communications through its networks. ODYSSEY THERAPEUTICS cannot be committed by this e-mail or warrant the accuracy or validity of any information presented. Any views expressed in this message are those of the individual sender.