: 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 >
90 (su
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: more thinking and less
pipetting (?)
Dear Randy,
Can you comment on why for some of AplhaFold2 models with G
e show pretty amazing agreement 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] Alpha
f its 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 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:
“ho
CP4BB@JISCMAIL.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 e
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 AplhaF
you can align 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] Al
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 model) the RMS_CA (backb
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 wel
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: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and
> l
n is 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
>
gt; 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
> Gesendet: Mittwoch, 9. Dezember 2020 11:14
> An: CCP4BB@JISCMAIL.AC.UK
>
vaerts
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
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: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less
pipetting (?)
on the day the news came out, I did won
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 monomer.
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 h
... 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 (?)
An exampl
Subject: Re: [ccp4bb] External: Re: [ccp4bb]
AlphaFold: more thinking and less pipetting (?)
There was a little bit of pre
things
> right that 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]
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 thinking and
-
> *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 (?)
>
>
> There was a little bit of press-release hype: the
r they're 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 thinki
ompany
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 less
pipetting (?)
My impression is that they haven’t published the code, and i
ubject: Re: [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 "ou
Since I didn’t actually read the press release (but “attended" the CASP event
instead where the results were discussed in a little more detail…) this is news
to me, but I’d agree that there is some hyperbole there.
Alphafold2 (it’s probably important to distinguish it from AlphaFold since it’s
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 AlphaFold system
achieves a median score of 92.4 GDT overall across all targets. This means
that our
Hi
It’s a bit more than science by press release - they took part in CASP14 where
they were given sequences but no other experimental data, and did significantly
better than the other homology modellers (who had access to the same data) when
judge by independent analysis. There were things wron
My impression is that they haven’t published the code, and it is science by
press-release. If one of us tried it, we would - rightly - get hounded out of
time.
Adrian
On 4 Dec 2020, at 15:57, Michel Fodje
mailto:michel.fo...@lightsource.ca>> wrote:
I think the results from AlphaFold2, alth
December 2020 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 3
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 structure is in the sequence. The protein folding problem is simply how
to go from a sequence to the 3D structure. This is not a compl
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