A quote comes to mind (I cannot resist) :
"Now, my own suspicion is that the universe is not only queerer than we
suppose, but queerer than we can suppose [...]"
-J. B. S. Haldane
"Possible Worlds"
in Possible Worlds and Other Essays (1927), p. 286
###
I absolutely agree with Guenter. This non experts speaking wrong things is
increasingly happening nowadays. Thanks Guenter, for pointing this out. A
theory unless it is given experimental data derived evidence it is still a
prediction (just like weather prediction, unless it is realised in the
p
We are getting the same feeling from discussions with (non-structural)
biologists around us.
I also agree that AlphaFold models are a great tool but they do not tell
everything and cannot exactly replace experiments.
Is the development mainly in the hands of journals' reviewers...?
Best,
Jan
O
Dear all,
taking AlphaFold models for " true" experimental structures seems to
become a serious problem.
I am just returning from a meeting (not a structural biology meeting)
and saw one model after other. And the non-structural biologist used
terms like "we calculated a structure" or "a Alph
Dear James,
I love your Star Trek Transporter analogy!
"Beam me up Scotty..." Oops!
Cheers,
Bill
From: "James Holton"
To: "CCP4BB"
Sent: Saturday, 15 April, 2023 01:28:35
Subject: Re: [ccp4bb] Structure prediction - waiting to happen
Very sorry to he
Very sorry to hear about your grant. I've been there. It is crushing to
be rejected, and frustrating when the reason given is ... wrong.
My journalist friends wonder why scientists don't like talking to
journalists. This is why. I remember when the first results from XFELs
were published, and
g
> Sent: Sunday, April 2, 2023 10:20 AM
> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting
> to happen
>
> EXTERNAL EMAIL: This e-mail is from a sender outside of the UTEP system. Do
> not clic
Subject: Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting to
happen
EXTERNAL EMAIL: This e-mail is from a sender outside of the UTEP system. Do not
click any links or open any attachments unless you trust the sender and know
the content is safe.
Please forward suspicious
letin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eugene Valkov <eugene.val...@gmail.com>
Sent: Sunday, April 2, 2023 10:10 AM
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting to happen
Predicted
stru
ructures.
> That’s more damaging than helpful.
>
>
> --
> *From:* CCP4 bulletin board on behalf of Eugene
> Valkov
> *Sent:* Sunday, April 2, 2023 10:10 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] [External] Re: [ccp4bb] Structur
M
*To:* CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>
*Subject:* [External] Re: [ccp4bb] Structure prediction - waiting
to happen
All, the first hurdle will of course be whether the AlphaFold
model works as a MR model, even with the 100% completeness and
sequen
, 2023 10:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting to
happen
Predicted structures lack the precision and accuracy of
experimentally-determined structures at high resolution with all the benefits
of unbiased co-discovery of
e.com/articles/s41401-022-00938-y
>
> --
> *From:* CCP4 bulletin board
> on behalf of Ian Tickle
>
> *Sent:* Sunday, April 2, 2023 8:28 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
>
> *Subject:* [External] Re: [ccp4bb] Structure prediction - waiting to
&g
prediction - waiting to
happen
All, the first hurdle will of course be whether the AlphaFold model
works as a MR model, even with the 100% completeness and sequence
identity of a bespoke model. The question is what B factors to use or
which disordered bits to leave out, as that can strongly
: CCP4BB@JISCMAIL.AC.UK
Subject: [External] Re: [ccp4bb] Structure prediction - waiting to happen
All, the first hurdle will of course be whether the AlphaFold model works as a
MR model, even with the 100% completeness and sequence identity of a bespoke
model. The question is what B factors to
variability,
and most of the systematic studies often exclude these tricky cases.
From: CCP4 bulletin board on behalf of Ian Tickle
Sent: Sunday, April 2, 2023 8:28 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [External] Re: [ccp4bb] Structure prediction - waiting to
cture prediction - waiting to happen
All, the first hurdle will of course be whether the AlphaFold model works as a
MR model, even with the 100% completeness and sequence identity of a bespoke
model. The question is what B factors to use or which disordered bits to leave
out, as that can str
All, the first hurdle will of course be whether the AlphaFold model works
as a MR model, even with the 100% completeness and sequence identity of a
bespoke model. The question is what B factors to use or which disordered
bits to leave out, as that can strongly influence the result (perhaps use
inf
Dear all,
I think that quoting general viewpoints and statements, however
knowledgeable and respected their authors may be, will only exacerbate the
climate of clashing prejudices between two camps and is bound to sustain a
war of opinions rather than lead to a rational acceptance that someth
I think this is all true - and I’ve been putting things like this into my
(failing) grants - but I get the dispiriting sense that the medics think (to
borrow a line from hamlet) “the applicant doth protest too much methinks”.
Well if as per James H today ;), we deposit coordinates to 1sf, alpha
There’s also this preprint with Tom Terwilliger as lead author:
https://www.biorxiv.org/content/10.1101/2022.11.21.517405v1. The title is
“AlphaFold predictions: great hypotheses but no match for experiment”.
Best wishes,
Randy
> On 1 Apr 2023, at 18:18, Savvas Savvides
> <9d24f7f13e09-dm
Dear Rams,
I salute you for sharing this.
Just a week ago, I also received a remark along these lines on a declined grant
application. The remark was the only unfavourable point, which suggested that
it must have weighed disproportionally towards the negative outcome. This was a
two-stage eval
I was afraid of this happening at some point and decided to start a new career
~ten years ago and use structures only as a tool and never put them into the
centerpiece of a grant.
My fall back option is either a cocktail bar or starting a restaurant. The
Triple M’s always work Mojito, Martini,
alphafold can replace the
need for experimental data.
Dhiraj
From: CCP4 bulletin board on behalf of Ian Tickle
Sent: Saturday, April 1, 2023 9:46 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [External] Re: [ccp4bb] Structure prediction - waiting to happen
Hi
Hi,
Just ask ChatGPT to write it for you!
Dale Tronrud
On 4/1/2023 5:06 AM, Subramanian, Ramaswamy wrote:
Dear All,
I am unsure if all other groups will get it - but I am sure this group
will understand the frustration.
My NIH grant did not get funded. A few genuine comments - they m
Ian,
Thank you. This is not an April fools..
Rams
subra...@purdue.edu
On Apr 1, 2023, at 10:46 AM, Ian Tickle wrote:
External Email: Use caution with attachments, links, or sharing data
Hi Ramaswamy
I assume this is an April Fool's but it's still a serious question because many
Hi Ramaswamy
I assume this is an April Fool's but it's still a serious question because
many reviewers who are not crystallographers or electron microscopists may
not fully appreciate the difference currently between the precision of
structures obtained by experimental and predictive methods, thou
" Is there a canned consensus paragraph that one can add with references to
grants "
How about:
“In general we look for a new law by the following process. First we guess it.
Then we compute the consequences of the guess to see what would be implied if
this law that we guessed is right. Then w
Dear All,
I am unsure if all other groups will get it - but I am sure this group will
understand the frustration.
My NIH grant did not get funded. A few genuine comments - they make excellent
sense. We will fix that.
One major comment is, “Structures can be predicted by alpfafold and other
29 matches
Mail list logo
