CCL: AlphaFold 3 vs AutoDock Vina

Maybe relevant - Not sure how true to the original AF3 implementation this
 is but given that DeepMind decided to make this closed source there has
 been some efforts from the open source community to implement AF3. See
 github link below:
 https://github.com/lucidrains/alphafold3-pytorch
 On Wed, Jun 26, 2024 at 1:51 PM Oleg Trott trott : caa.columbia.edu <
 owner-chemistry*|*ccl.net> wrote:
 >
 > Sent to CCL by: Oleg Trott [trott:+:caa.columbia.edu]
 > Thanks!
 >
 > I hope someone re-runs DeepMind's calculations, with the same
 > settings, but using k-fold cross-validation (like what I did at
 > Columbia), where test and training sets are never related. This will
 > show how well (or poorly, as the case may be) the method generalizes
 > to unrelated proteins.
 >
 >
 > =====
 > Oleg Trott, PhD
 > https://olegtrott.com
 >
 >
 >
 >
 >
 > On Tue, Jun 25, 2024 at 11:31 AM Aydin Manzouri aydin.manzouri ~~
 > gmail.com <owner-chemistry_-_ccl.net> wrote:
 > >
 > > Truly insightful. Thanks a lot.
 > >
 > > On Tue, Jun 25, 2024 at 1:59 AM Oleg Trott
 trott[-]caa.columbia.edu
 > <owner-chemistry*_*ccl.net> wrote:
 > >>
 > >>
 > >> Sent to CCL by: "Oleg  Trott" [trott-$-caa.columbia.edu]
 > >> Hello, everyone!
 > >>
 > >> DeepMind's new AlphaFold 3 attempts to predict protein-ligand
 binding,
 > and
 > >> their publication compares it to AutoDock Vina (which I built).
 But
 > their
 > >> methodology seems strange.
 > >>
 > >> I wrote up my comments in a blog post. If you have an interest in
 AI
 > and/or
 > >> docking, I hope you'll find it insightful.
 > >>
 > >> https://olegtrott.substack.com/p/are-alphafolds-new-results-a-miracle>>;
 > E-mail to subscribers: CHEMISTRY*_*ccl.net or use:>>
 > >> E-mail to administrators: CHEMISTRY-REQUEST*_*ccl.net or
 use>>
 > >>
 >
 >
 >
 > -= This is automatically added to each message by the mailing script =->
 >
 >