On Dec 3, 2020, at 4:16 PM, Peat, Tom (Manufacturing, Parkville)
<tom.p...@csiro.au <mailto:tom.p...@csiro.au>> wrote:
Although they can now get the fold correct, I don't think they have
all the side chain placement so perfect as to be able to predict the
fold_and_how a compound or another protein binds, so we can still do
complexes. I don't know what others end up spending their time doing,
but much of my work has been trying to fit ligands into density,
which may take another few years of algorithm development, which is
fine for me as I can retire!
cheers, tom
Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au <mailto:tom.p...@csiro.au>
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*From:*CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Jon Cooper
<0000488a26d62010-dmarc-requ...@jiscmail.ac.uk
<mailto:0000488a26d62010-dmarc-requ...@jiscmail.ac.uk>>
*Sent:*Friday, December 4, 2020 9:55 AM
*To:*CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK><CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>>
*Subject:*Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)
Thanks all, very interesting, so our methods are just needed to
identify the crystallization impurities, when the trays have been
thrown away ;-
Cheers, Jon.C.
Sent from ProtonMail mobile
-------- Original Message --------
On 3 Dec 2020, 22:31, Anastassis Perrakis <a.perra...@nki.nl
<mailto:a.perra...@nki.nl>> wrote:
AlphaFold - or similar ideas that will surface up sooner or later
- will beyond doubt have major impact. The accuracy it
demonstrated compared to others is excellent.
“Our” target (T1068) that was not solvable by MR with the
homologous search structure or a homology model (it was phased
with Archimboldo, rather easily), is easily solvable with
the AlphaFold model as a search model. In PHASER I get Rotation
Z-score 17.9, translation Z-score 26.0, using defaults.
imho what remains to be seen is:
a. how and when will a prediction server be available?
b. even if training needs computing that will surely unaccessible
to most, will there be code that can be installed in a
“reasonable” number of GPUs and how fast will it be?
c. how do model quality metrics (that do not compared with the
known answer) correlate with the expected RMSD? AlphaFold, no
matter how impressive, still gets things wrong.
c. will the AI efforts now gear to ligand (fragment?) prediction
with similarly impressive performance?
Exciting times.
A.
On 3 Dec 2020, at 21:55, Jon Cooper
<0000488a26d62010-dmarc-requ...@jiscmail.ac.uk
<mailto:0000488a26d62010-dmarc-requ...@jiscmail.ac.uk>> wrote:
Hello. A quick look suggests that a lot of the test structures
were solved by phaser or molrep, suggesting it is a very welcome
improvement on homology modelling. It would be interesting to
know how it performs with structures of new or uncertain fold,
if there are any left these days. Without resorting to jokes
about artificial intelligence, I couldn't make that out from the
CASP14 website or the many excellent articles that have
appeared. Best wishes, Jon Cooper.
Sent from ProtonMail mobile
-------- Original Message --------
On 3 Dec 2020, 11:17, Isabel Garcia-Saez <isabel.gar...@ibs.fr
<mailto:isabel.gar...@ibs.fr>> wrote:
Dear all,
Just commenting that after the stunning performance of
AlphaFold that uses AI from Google maybe some of us we could
dedicate ourselves to the noble art of gardening, baking,
doing Chinese Calligraphy, enjoying the clouds pass or
everything together (just in case I have already prepared my
subscription to Netflix).
https://www.nature.com/articles/d41586-020-03348-4
<https://www.nature.com/articles/d41586-020-03348-4>
Well, I suppose that we still have the structures of
complexes (at the moment). I am wondering how the labs will
have access to this technology in the future (would it be
for free coming from the company DeepMind - Google?). It
seems that they have already published some code. Well,
exciting times.
Cheers,
Isabel
Isabel Garcia-SaezPhD
Institut de Biologie Structurale
Viral Infection and Cancer Group (VIC)-Cell Division Team
71, Avenue des Martyrs
CS 10090
38044 Grenoble Cedex 9
France
Tel.: 00 33 (0) 457 42 86 15
e-mail: isabel.gar...@ibs.fr <mailto:isabel.gar...@ibs.fr>
FAX: 00 33 (0) 476 50 18 90
http://www.ibs.fr/ <http://www.ibs.fr/>
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