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
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
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
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
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
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
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