of
Leonid Sazanov
Sent: 11 December 2020 10:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more
thinking and less pipetting (?)
Dear Randy,
Can you comment on why for some of AplhaFold2 models with GDT_TS >
90 (supposedly as good as experimental mo
A.
From: CCP4 bulletin board on behalf of Leonid Sazanov
Sent: 11 December 2020 10:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
Dear Randy,
Can you comment on why for some of AplhaFold2 models with GDT_TS >
eement with the target.
Best regards,
Tristan
*From:* Leonid Sazanov
*Sent:* 11 December 2020 12:32
*To:* Tristan Croll ; CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more
thinking and
crystallization -
and if it is only: difficult!
Best,
Hans
-Original Message-
From: CCP4 bulletin board On Behalf Of Bryan Lepore
Sent: Freitag, 11. Dezember 2020 15:03
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
> On
> On Dec 11, 2020, at 07:42, Phil Evans wrote:
>
> But I’ve always thought the more interesting question is “this is the
> structure, what does it do?”
It sounds compelling though, that methods of the sort implemented in the CASP
work are perfectly poised to make progress on the question:
MAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
Dear Randy,
Can you comment on why for some of AplhaFold2 models with GDT_TS > 90
(supposedly as good as experimenta
tin board on behalf of Leonid Sazanov
>
> Sent: 11 December 2020 10:36
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and
> less pipetting (?)
>
> Dear Randy,
>
> Can you comment on why for some of AplhaFold2 model
ign 109 of 134 CAs with an RMSD of
0.46 A.
*From:* CCP4 bulletin board on behalf of
Leonid Sazanov
*Sent:* 11 December 2020 10:36
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: m
December 2020 10:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
Dear Randy,
Can you comment on why for some of AplhaFold2 models with GDT_TS > 90
(supposedly as good as experimental model) the RMS_CA (backbone) is &g
Dear Randy,
Can you comment on why for some of AplhaFold2 models with GDT_TS > 90
(supposedly as good as experimental model) the RMS_CA (backbone) is > 3.0
Angstrom? Such a deviation can hardly be described as good as experimental.
Could it be that GDT_TS is kind of designed to evaluate how
t hope i'm
> wrong!
> best
> jon
>
> Von: CCP4 bulletin board Im Auftrag von Mark J van
> Raaij
> Gesendet: Mittwoch, 9. Dezember 2020 11:14
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and
> less
> On Dec 9, 2020, at 07:45, Harry Powell - CCP4BB
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> ... GDT_TS (Global Distance Test - Total Score - you can look it up on
> Wikipedia
Thanks, this is helpful.
Wikipedia:
“The primary GDT assessment uses only the alpha carbon
that this is a virtual infectious disease
> that will cause humanity far bigger problems than corona ever will – i just
> hope i'm wrong!
> >
> > best
> >
> > jon
> >
> >
> >
> > Von: CCP4 bulletin board Im Auftrag von Mark J
> van Raaij
> > Ges
The “something” is what gives them their edge (and which they’ve hinted at, but
avoided being explicit)…
The main quality score used to distinguish their results is GDT_TS (Global
Distance Test - Total Score - you can look it up on Wikipedia like I did).
Although it doesn’t say in Wikipedia,
On Dec 9, 2020, at 07:16, Harry Powell wrote:
>
> ...the important thing is [...] they’ve done something that no-one else has
> managed to do as well in spite of years of trying.
What, precisely, is the “something”?
Exactly how much better than second place?
Was the scoring the same across
ause humanity far bigger problems than corona ever will – i just hope i'm
> wrong!
>
> best
>
> jon
>
>
>
> Von: CCP4 bulletin board Im Auftrag von Mark J van
> Raaij
> Gesendet: Mittwoch, 9. Dezember 2020 11:14
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff:
Sent: Wednesday, December 9, 2020 9:37:17 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
Dear All
After about 10 (!) years of (very) hard work we solved the structures of our
dearest membrane transporter. Dataset at 2.9 And
hope i'm wrong!
best
jon
Von: CCP4 bulletin board Im Auftrag von Mark J van Raaij
Gesendet: Mittwoch, 9. Dezember 2020 11:14
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
on the day the news came out, I did wonder
on the day the news came out, I did wonder if the AlphaFold2 team somehow had
access to all the preliminary PDB files sent around via Gmail (which belongs to
the same company), but more as a joke/conspirational thought.
"our" target T1052, was also predicted very well by domains and as a
Dear All
After about 10 (!) years of (very) hard work we solved the structures of our
dearest membrane transporter. Dataset at 2.9 And resolution, fairly
anisotropic, experimental phasing, and many long nights with Coot and
Buster to achieve model refinement.
The experimental structure
... and of course I meant "between model and target".
From: Tristan Croll
Sent: 08 December 2020 16:35
To: CCP4BB@JISCMAIL.AC.UK ; Marko Hyvonen
Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
4bb] External: Re: [ccp4bb]
AlphaFold: more thinking and less pipetting (?)
There was a little bit of press-release
Greetings — I am interested to know more about the following points to
understand the results :
[1] How was the “C-alpha-IDDT” (Mariani et. al., Bioinformatics, 29(21),
2722-2728, 2013) used, as - if I understand, the unprecedented and exceptional
prediction capabilities of AlphaFold2 - as
, 08 Dec 2020 15:15:14 +0200 (EET)
Subject: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)
Dear Isabel,
My article in the IUCr Newsletter on DeepMind and CASP14 is released today and
can be found here:-
https://www.iucr.org/news/newsletter/volume-28/number-4/deepmind-and-casp14
Best
at are wrong in the experimental structure.
> --
> *From:* CCP4 bulletin board
> on behalf of Ian Tickle
>
> *Sent:* 08 December 2020 13:04
> *To:* CCP4BB@JISCMAIL.AC.UK
>
> *Subject:* Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thin
structure.
From: CCP4
bulletin board on behalf of Ian
Tickle
Sent: 08 December 2020 13:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold:
more thinking and less pipetting
CCP4 bulletin board on behalf of Ian
> Tickle
> *Sent:* 08 December 2020 13:04
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking
> and less pipetting (?)
>
>
> There was a little bit of press-release hype: the release stated
a private company
>
> best
>
> jon
>
>
>
> *Von:* CCP4 bulletin board *Im Auftrag von *Goldman,
> Adrian
> *Gesendet:* Dienstag, 8. Dezember 2020 12:33
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking
> and les
jon
Von: CCP4 bulletin board Im Auftrag von Goldman, Adrian
Gesendet: Dienstag, 8. Dezember 2020 12:33
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
My impression is that they haven’t published the code, and it is science
: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
There was a little bit of press-release hype: the release stated "a score of
around 90 GDT is informally considered to be competitive with results obtained
from experimental methods" and "our latest A
structure can be gleaned in bits and pieces scattered
> >> between homologous sequences, multiple-sequence alignments, and other
> >> protein 3D structures in the PDB. Deep Learning allows a huge amount of
> >> data to be thrown at a problem and the back-propagation o
Dear Isabel,
My article in the IUCr Newsletter on DeepMind and CASP14 is released today and
can be found here:-
https://www.iucr.org/news/newsletter/volume-28/number-4/deepmind-and-casp14
Best wishes,
John
Emeritus Professor John R Helliwell DSc
> On 3 Dec 2020, at 11:17, Isabel Garcia-Saez
gt; information are to the prediction. The networks used here are humongous
> and a detailed look at the weights (if at all feasible) may point us in the
> right direction.
> >>
> >>
> >> From: CCP4 bulletin board On Behalf Of Nave,
> Colin (DLSLtd,RAL,LSCI)
>
mine how relevant different pieces of information are to the
>> prediction. The networks used here are humongous and a detailed look at the
>> weights (if at all feasible) may point us in the right direction.
>>
>>
>> From: CCP4 bulletin board On Behalf Of Nave, Colin
>&g
board mailto:CCP4BB@JISCMAIL.AC.UK>>
On Behalf Of Nave, Colin (DLSLtd,RAL,LSCI)
Sent: December 4, 2020 9:14 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)
The subject line for Isabel’s email i
020 15:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
I think the results from AlphaFold2, although exciting and a breakthrough are
being exaggerated just a bit. We know that all the information required for
the 3D structur
Run it for more cycles. Doesn't take long to drift far enough for it to
not find its way back when you turn x-ray back on.
This isn't just a problem in refmac, or phenix, or x-plor, or even MD
programs like AMBER. The problem is that in order to make a structure
fit into density you have to
the right direction.
From: CCP4 bulletin board On Behalf Of Nave, Colin
(DLSLtd,RAL,LSCI)
Sent: December 4, 2020 9:14 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)
The subject line for Isabel's email is very good.
I do have a ques
The subject line for Isabel's email is very good.
I do have a question (more a request) for the more computer scientist oriented
people. I think it is relevant for where this technology will be going. It
comes from trying to understand whether problems addressed by Alpha are NP, NP
hard, NP
Hi Frank,
Yes, until CASP7 (back in 2006), I used to like saying that there are many more
ways to make a homology model worse than the starting template than to make it
better, and that homology modelling programs were very good at finding them!
After seeing that at least some models (e.g.
I guess that also means that AlphaFold has learnt the
crystal-structure-ness that older homology methods never achieved -
which is why (anecdotally?) a "better" homology model tended to give
worse MR performance than the "worse" template?
(Or something like that, I'm parrotting what I
I thought I might be able to add a little to this conversation as I performed
some MR runs as part of the CASP14 High Accuracy analysis. There were 30
targets with reflection data. Of these, AlphaFold2 models could be used to
directly solve 24 structures after converting
RMS error predictions
optimisation, but
that's not the case just yet.
Best
John
From: CCP4 bulletin board on behalf of Jan Löwe
Sent: 04 December 2020 10:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)
AlphaFold2 and its
Hi James,
One really interesting (and to me surprising) aspect of how well AlphaFold2
does is that it does really well without actually understanding chemistry and
physics. (John Jumper from DeepMind talked about choices of deep learning
model types and how they affect the “inductive bias”
behalf of Jon Cooper
<488a26d62010-dmarc-requ...@jiscmail.ac.uk
<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk>>
*Sent:*Friday, December 4, 2020 9:55 AM
*To:*CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK><mailto:CCP4BB@JISCMAIL.AC.UK>>
*Subject
décembre 2020 10:15
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)
Exciting times, indeed. I haven’t looked through the results myself, but it
does look like an extraordinary advance. I wonder though how this advance
correlates with ‘understanding
Exciting times, indeed. I haven’t looked through the results myself, but it
does look like an extraordinary advance. I wonder though how this advance
correlates with ‘understanding’ how proteins folds. Can these outstanding
results be distilled in a set of improved principles for how proteins
Dear Boaz,
The archimboldo model gives Rot z-score: 8.1, Trans Z-score 13.8
Not sure this matters, as it lacks a few loops that even good old arp/warp can
fill up in ten minutes ;-)
A.
On Dec 4, 2020, at 0:40, Boaz Shaanan
mailto:bshaa...@bgu.ac.il>> wrote:
Just curious, how does the result
hursday, December 3, 2020 5:31 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [EXTERNAL] Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)
AlphaFold - or similar ideas that will surface up sooner or later - will beyond
doubt have major impact. The
---
*From:* CCP4 bulletin board on behalf of
Anastassis Perrakis
*Sent:* Thursday, December 3, 2020 5:31 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [EXTERNAL] Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
AlphaFold - or similar ideas that will surface up sooner or later -
I'm curious how well AlphaFold would do on an Intrinsically Disordered Protein
(IDP),
would it recognize that it is an "IDP" or predict that it has a structure (or
structures)?
It would be interesting to test such a sequence and see what comes out.
Possibly AlphaFold might be the best IDP
Hello James, that's really strange - I've used refmac et al., to do poor man's
energy minimizations of models and they've generally come out fine, unless the
restraints, etc, are wildly off-target. I wasn't playing with X-ray weights
though, since there never was a dataset, of course.
Cheers,
It is a major leap forward for structure prediction for sure. A hearty
congratulations to all those teams over all those years.
The part I don't understand is the accuracy. If we understand what
holds molecules together so well, then why is it that when I refine an
X-ray structure and turn
> <mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk>>
> Sent: Friday, December 4, 2020 9:55 AM
> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> mailto:CCP4BB@JISCMAIL.AC.UK>>
> Subject: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?
From: CCP4 bulletin board on behalf of Jon Cooper
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Sent: Friday, December 4, 2020 9:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)
Thanks all, very inter
Just curious, how does the result of the Phaser run with the Alphafold model compare with a Phaser run using the Arcimboldo phased model as a probe?
Boaz
Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel
On Dec 4, 2020 00:32, Anastassis
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 wrote:
> AlphaFold - or
and Biochemistry
New York, NY 10031
From: CCP4 bulletin board on behalf of Anastassis
Perrakis
Sent: Thursday, December 3, 2020 5:31 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)
AlphaFold - or similar
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
9662 7304
+614 57 539 419
tom.p...@csiro.au
From: CCP4 bulletin board on behalf of Jon Cooper
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Sent: Friday, December 4, 2020 7:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AlphaFold: more thinking an
10-dmarc-requ...@jiscmail.ac.uk>
À: "CCP4BB"
Envoyé: Jeudi 3 Décembre 2020 21:55:38
Objet: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)
Hello. A quick look suggests that a lot of the test structures were solved by
phaser or molrep, suggesting it is a very welcome improvem
A quick note regarding the code that Deepmind released for CASP13 (2018).
It bears the rather important caveat that: "This code can't be used to predict
structure of an arbitrary protein sequence. It can be used to predict structure
only on the CASP13 dataset (links below)."
Source:
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
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