Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

2023-12-01 Thread Mark J. van Raaij 
just came across this critique of that paper on Twitter:

https://twitter.com/Robert_Palgrave/status/1730358675523424344 
Robert Palgrave (@Robert_Palgrave) on X
twitter.com

https://twitter.com/Robert_Palgrave/status/1730358675523424344but I'm not 
enough of an expert to judge - perhaps some characterizations were wrong and a 
lot of the paper does stand.


> On 1 Dec 2023, at 20:51, Bryan Lepore  wrote:
> 
> Adding to that literature list a bit outside :
> 
> Merchant, A., Batzner, S., Schoenholz, S.S. et al. 
> 
> Quote:
> 
> "... we show that graph networks trained at scale can reach unprecedented 
> levels of generalization, improving the efficiency of materials discovery by 
> an order of magnitude. "
> 
> Scaling deep learning for materials discovery. 
> 
> Nature (2023), November
> 
> https://doi.org/10.1038/s41586-023-06735-9
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

2023-12-01 Thread Bryan Lepore 
Adding to that literature list a bit outside :

Merchant, A., Batzner, S., Schoenholz, S.S. et al. 

Quote:

"... we show that graph networks trained at scale can reach unprecedented 
levels of generalization, improving the efficiency of materials discovery by an 
order of magnitude. "

Scaling deep learning for materials discovery. 

Nature (2023), November

https://doi.org/10.1038/s41586-023-06735-9




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

2023-12-01 Thread Debanu Das 
Hi Tom,

Great to see your new analysis and publication. A wonderful addition to
your recent work in this domain/comparisons. Congratulations!

For those trying to keep up with "AI Drug Discovery" (including AlphaFold,
OpenFold, Gen AI, etc) vs "Conventional Drug Discovery" (primarily
crystallography/CryoEM/structural biology/biophysics for this audience), a
few recent papers and news items:

"AI’s potential to accelerate drug discovery needs a reality check"
https://www.nature.com/articles/d41586-023-03172-6

"Sumitomo Schizophrenia Drug Discovered With AI Tech Fails in Two Phase 3
Trials"
https://medcitynews.com/2023/07/sumitomo-schizophrenia-ai-drug-discovery-in-two-clinical-trial/

"AI-created drugs fall off hype cycle"
https://www.beckershospitalreview.com/pharmacy/ai-created-drugs-fall-off-hype-cycle.html

"After years of hype, the first AI-designed drugs fall short in the clinic"
https://endpts.com/first-ai-designed-drugs-fall-short-in-the-clinic-following-years-of-hype/

As a research community, while it is great to see new sci & tech maturing
and adding to the R, it's quite likely that when the dust settles (as
we've seen with many hypes, I think there are ~200 companies of different
sizes and stages claiming to be in the "AI" space, most with undisclosed
and unvalidated methods and approaches), all this could become a strong
*addition* to the drug discovery/structural biology arsenal, *instead of
substituting workhorse solutions and approaches*, potentially *most useful
in cases only when experimental structures are not available or not
immediately possible to kick off the start of projects*.

Best regards,
Debanu
--
Debanu Das,
https://bio.site/debanu_das

On Fri, Dec 1, 2023 at 10:23 AM Mitchell D. Miller <
mitchell.d.mil...@rice.edu> wrote:

> The Baker group has also reported substantial progress in all atom
> predictions
>
> Krishna et al.,
> Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom
> bioRxiv 2023.10.09.561603
> doi: 10.1101/2023.10.09.561603
> https://www.biorxiv.org/content/10.1101/2023.10.09.561603v1.full
>
> Regards,
> Mitch
>
> Quoting Tom Terwilliger :
>
> > Hi Roberto,
> > Thanks for the link to the DeepMind site!  I hadn't seen that and now I
> > read it and the paper that they link to.  It looks to me as though they
> are
> > making significant progress on ligands, dna, rna, but that the program is
> > not yet available, so I don't think it can be tested yet!
> > All the best,
> > Tom T
> >
> >
> > On Fri, Dec 1, 2023 at 5:19 AM Roberto Steiner <
> roberto.stei...@kcl.ac.uk>
> > wrote:
> >
> >> Great paper indeed!
> >>
> >> However quite significant progress seems to have been achieved with
> >> ligands as well (and not only)…
> >>
> >>
> https://urldefense.com/v3/__https://deepmind.google/discover/blog/a-glimpse-of-the-next-generation-of-alphafold/__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GM9FxbyWs$
> >> Has anyone in the community put this to the test?
> >>
> >>
> >> Best wishes
> >> Roberto
> >>
> >>
> >> *Roberto A Steiner*
> >>
> https://urldefense.com/v3/__http://www.steinerlab.org__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMxbA8Qgg$
> >>
> https://urldefense.com/v3/__https://twitter.com/steiner_lab__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMZmS2rX0$
> >>
> >> roberto.stei...@kcl.ac.uk
> >> Randall Centre for Cell and Molecular Biophysics
> >> Faculty of Life Sciences and Medicine
> >> King's College London
> >> Room 3.10A
> >> New Hunt's House, Guy's Campus
> >> SE1 1UL, London, UK
> >> Phone 0044 20 78488216
> >> Fax0044 20 78486435
> >>
> >> roberto.stei...@unipd.it
> >> Dipartimento di Scienze Biomediche
> >> Università degli Studi di Padova
> >> Viale G. Colombo 3
> >> 35131 Padova, Italia
> >> Telefono 0039 049 8276409
> >>
> >> *Responses to emails are not expected outside of your normal working
> >> hours.*
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> On 30 Nov 2023, at 22:35, Tom Terwilliger <
> >> b6116340b489-dmarc-requ...@jiscmail.ac.uk> wrote:
> >>
> >> You don't often get email from
> >> b6116340b489-dmarc-requ...@jiscmail.ac.uk. Learn why this is
> important
> >> 
> >> Hi Structural biologist colleagues!
> >>
> >> Our article that helps you make the case that the experiment is still
> very
> >> much needed is now out:
> >>
> >> https://www.nature.com/articles/s41592-023-02087-4
> >>
> >> "AlphaFold predictions are valuable hypotheses and accelerate but do not
> >> replace experimental structure determination."  Nature Methods (2023)
> >>
> >> Also, here is a video on the Phenix Tutorials YouTube channel that
> >> describes this analysis:
> >>
>

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

2023-12-01 Thread Mitchell D. Miller 

The Baker group has also reported substantial progress in all atom predictions

Krishna et al.,
Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom
bioRxiv 2023.10.09.561603
doi: 10.1101/2023.10.09.561603
https://www.biorxiv.org/content/10.1101/2023.10.09.561603v1.full

Regards,
Mitch

Quoting Tom Terwilliger :


Hi Roberto,
Thanks for the link to the DeepMind site!  I hadn't seen that and now I
read it and the paper that they link to.  It looks to me as though they are
making significant progress on ligands, dna, rna, but that the program is
not yet available, so I don't think it can be tested yet!
All the best,
Tom T


On Fri, Dec 1, 2023 at 5:19 AM Roberto Steiner 
wrote:


Great paper indeed!

However quite significant progress seems to have been achieved with
ligands as well (and not only)…

https://urldefense.com/v3/__https://deepmind.google/discover/blog/a-glimpse-of-the-next-generation-of-alphafold/__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GM9FxbyWs$
Has anyone in the community put this to the test?


Best wishes
Roberto


*Roberto A Steiner*
https://urldefense.com/v3/__http://www.steinerlab.org__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMxbA8Qgg$
https://urldefense.com/v3/__https://twitter.com/steiner_lab__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMZmS2rX0$

roberto.stei...@kcl.ac.uk
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London
Room 3.10A
New Hunt's House, Guy's Campus
SE1 1UL, London, UK
Phone 0044 20 78488216
Fax0044 20 78486435

roberto.stei...@unipd.it
Dipartimento di Scienze Biomediche
Università degli Studi di Padova
Viale G. Colombo 3
35131 Padova, Italia
Telefono 0039 049 8276409

*Responses to emails are not expected outside of your normal working
hours.*








On 30 Nov 2023, at 22:35, Tom Terwilliger <
b6116340b489-dmarc-requ...@jiscmail.ac.uk> wrote:

You don't often get email from
b6116340b489-dmarc-requ...@jiscmail.ac.uk. Learn why this is important

Hi Structural biologist colleagues!

Our article that helps you make the case that the experiment is still very
much needed is now out:

https://www.nature.com/articles/s41592-023-02087-4

"AlphaFold predictions are valuable hypotheses and accelerate but do not
replace experimental structure determination."  Nature Methods (2023)

Also, here is a video on the Phenix Tutorials YouTube channel that
describes this analysis:   
https://urldefense.com/v3/__https://www.youtube.com/watch?v=ugMPYdPo8Bc__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMqp4wPP4$


(I hope you will be happy to see that you and your structural biology
colleagues get the credit for making AlphaFold possible at 2:35 in the
introduction of this video!  Keep up the fantastic structural biology work!)

All the best,
Tom T
--
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilli...@newmexicoconsortium.org
Tel: 505-431-0010


--

To unsubscribe from the CCP4BB list, click the following link:
https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMTS3GjrY$





--
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilli...@newmexicoconsortium.org
Tel: 505-431-0010



To unsubscribe from the CCP4BB list, click the following link:
https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMTS3GjrY$

This message was issued to members of  
https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GM6b0LSR0$ , a mailing list hosted by https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GMrJES6CY$ , terms & conditions are available at  
https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!BuQPrrmRaQ!mWTLfJ8Bjj3YYdp1ZCa8HXyjF-1lq1emf12VPcusoqMN5sh4Eajgq-3UOcaWAERlTNpVWXSdqVPUzhyjIYzPrkIn0P-gtdIjb9GM_4rhs78$

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

2023-12-01 Thread Eleanor Dodson 
Very very interesting analysis - Thankyou!

On Fri, 1 Dec 2023 at 18:01, Tom Terwilliger <
b6116340b489-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Roberto,
> Thanks for the link to the DeepMind site!  I hadn't seen that and now I
> read it and the paper that they link to.  It looks to me as though they are
> making significant progress on ligands, dna, rna, but that the program is
> not yet available, so I don't think it can be tested yet!
> All the best,
> Tom T
>
>
> On Fri, Dec 1, 2023 at 5:19 AM Roberto Steiner 
> wrote:
>
>> Great paper indeed!
>>
>> However quite significant progress seems to have been achieved with
>> ligands as well (and not only)…
>>
>> https://deepmind.google/discover/blog/a-glimpse-of-the-next-generation-of-alphafold/
>> Has anyone in the community put this to the test?
>>
>>
>> Best wishes
>> Roberto
>>
>>
>> *Roberto A Steiner*
>> www.steinerlab.org
>> https://twitter.com/steiner_lab
>>
>> roberto.stei...@kcl.ac.uk
>> Randall Centre for Cell and Molecular Biophysics
>> Faculty of Life Sciences and Medicine
>> King's College London
>> Room 3.10A
>> New Hunt's House, Guy's Campus
>> SE1 1UL, London, UK
>> Phone 0044 20 78488216
>> Fax0044 20 78486435
>>
>> roberto.stei...@unipd.it
>> Dipartimento di Scienze Biomediche
>> Università degli Studi di Padova
>> 
>> Viale G. Colombo 3
>> 
>> 35131 Padova, Italia
>> Telefono 0039 049 8276409
>>
>> *Responses to emails are not expected outside of your normal working
>> hours.*
>>
>>
>>
>>
>>
>>
>>
>>
>> On 30 Nov 2023, at 22:35, Tom Terwilliger <
>> b6116340b489-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> You don't often get email from
>> b6116340b489-dmarc-requ...@jiscmail.ac.uk. Learn why this is
>> important 
>> Hi Structural biologist colleagues!
>>
>> Our article that helps you make the case that the experiment is still
>> very much needed is now out:
>>
>> https://www.nature.com/articles/s41592-023-02087-4
>>
>> "AlphaFold predictions are valuable hypotheses and accelerate but do not
>> replace experimental structure determination."  Nature Methods (2023)
>>
>> Also, here is a video on the Phenix Tutorials YouTube channel that
>> describes this analysis:  https://www.youtube.com/watch?v=ugMPYdPo8Bc
>>
>> (I hope you will be happy to see that you and your structural biology
>> colleagues get the credit for making AlphaFold possible at 2:35 in the
>> introduction of this video!  Keep up the fantastic structural biology work!)
>>
>> All the best,
>> Tom T
>> --
>> Thomas C Terwilliger
>> Laboratory Fellow, Los Alamos National Laboratory
>> Senior Scientist, New Mexico Consortium
>> 100 Entrada Dr, Los Alamos, NM 87544
>> 
>> Email: tterwilli...@newmexicoconsortium.org
>> Tel: 505-431-0010
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>>
>>
>
> --
> Thomas C Terwilliger
> Laboratory Fellow, Los Alamos National Laboratory
> Senior Scientist, New Mexico Consortium
> 100 Entrada Dr, Los Alamos, NM 87544
> 
> Email: tterwilli...@newmexicoconsortium.org
> Tel: 505-431-0010
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

2023-12-01 Thread Tom Terwilliger 
Hi Roberto,
Thanks for the link to the DeepMind site!  I hadn't seen that and now I
read it and the paper that they link to.  It looks to me as though they are
making significant progress on ligands, dna, rna, but that the program is
not yet available, so I don't think it can be tested yet!
All the best,
Tom T


On Fri, Dec 1, 2023 at 5:19 AM Roberto Steiner 
wrote:

> Great paper indeed!
>
> However quite significant progress seems to have been achieved with
> ligands as well (and not only)…
>
> https://deepmind.google/discover/blog/a-glimpse-of-the-next-generation-of-alphafold/
> Has anyone in the community put this to the test?
>
>
> Best wishes
> Roberto
>
>
> *Roberto A Steiner*
> www.steinerlab.org
> https://twitter.com/steiner_lab
>
> roberto.stei...@kcl.ac.uk
> Randall Centre for Cell and Molecular Biophysics
> Faculty of Life Sciences and Medicine
> King's College London
> Room 3.10A
> New Hunt's House, Guy's Campus
> SE1 1UL, London, UK
> Phone 0044 20 78488216
> Fax0044 20 78486435
>
> roberto.stei...@unipd.it
> Dipartimento di Scienze Biomediche
> Università degli Studi di Padova
> Viale G. Colombo 3
> 35131 Padova, Italia
> Telefono 0039 049 8276409
>
> *Responses to emails are not expected outside of your normal working
> hours.*
>
>
>
>
>
>
>
>
> On 30 Nov 2023, at 22:35, Tom Terwilliger <
> b6116340b489-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> You don't often get email from
> b6116340b489-dmarc-requ...@jiscmail.ac.uk. Learn why this is important
> 
> Hi Structural biologist colleagues!
>
> Our article that helps you make the case that the experiment is still very
> much needed is now out:
>
> https://www.nature.com/articles/s41592-023-02087-4
>
> "AlphaFold predictions are valuable hypotheses and accelerate but do not
> replace experimental structure determination."  Nature Methods (2023)
>
> Also, here is a video on the Phenix Tutorials YouTube channel that
> describes this analysis:  https://www.youtube.com/watch?v=ugMPYdPo8Bc
>
> (I hope you will be happy to see that you and your structural biology
> colleagues get the credit for making AlphaFold possible at 2:35 in the
> introduction of this video!  Keep up the fantastic structural biology work!)
>
> All the best,
> Tom T
> --
> Thomas C Terwilliger
> Laboratory Fellow, Los Alamos National Laboratory
> Senior Scientist, New Mexico Consortium
> 100 Entrada Dr, Los Alamos, NM 87544
> Email: tterwilli...@newmexicoconsortium.org
> Tel: 505-431-0010
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
>

-- 
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilli...@newmexicoconsortium.org
Tel: 505-431-0010



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] CCP4 Study Weekend 2024 - In-person registration CLOSES MONDAY 4TH DECEMBER!

2023-12-01 Thread Karen McIntyre - STFC UKRI 
In-person registration for the CCP4 Study Weekend 2024 closes on Monday 4th 
December (this coming Monday).

Virtual registration will still be available after this date.

Register now if you want to be in the room where it happens!

Regards

Karen McIntyre

CCP4 Project Administrator
CCP4 Equality, Diversity and Inclusion Champion
Member of SCD ED Working Group

Science and Technology Facilities Council
karen.mcint...@stfc.ac.uk
Zoom phone: 01235 44 5790

[cid:image001.png@01DA2463.11ADDC60]

**Hours of work: Monday to Thursday: 8.30am to 1.30pm, Friday 10:30am to 
3.30pm.  Please note that I only work part-time **

From: McIntyre, Karen (STFC,RAL,SC)
Sent: Thursday, November 23, 2023 12:21 PM
To: 'ccp4bb' ; CCP4 WG1 ; 
CCP4 WG2 ; 'cc...@jiscmail.ac.uk' 
; 'c...@jiscmail.ac.uk' ; 
'pheni...@phenix-online.org' ; 
'pdbe-api-us...@ebi.ac.uk' 
Subject: RE: CCP4 Study Weekend 2024 - In-person Early bird registration 
including standard student bursary CLOSES TODAY!
Importance: High

In-person early bird registration for the CCP4 Study Weekend 2024 closes today.

Anyone registering for the in-person event after today will not be eligible for 
a standard student bursary and the price for standard delegates increases by 
£50.

In-person registration will close on Monday 4th December 2023.

Virtual registration will still be available after this date.

Regards

Karen McIntyre

CCP4 Project Administrator
CCP4 Equality, Diversity and Inclusion Champion
Member of SCD ED Working Group

Science and Technology Facilities Council
karen.mcint...@stfc.ac.uk
Zoom phone: 01235 44 5790

[cid:image001.png@01DA2463.11ADDC60]

**Hours of work: Monday to Thursday: 8.30am to 1.30pm, Friday 10:30am to 
3.30pm.  Please note that I only work part-time **

From: McIntyre, Karen (STFC,RAL,SC)
Sent: Tuesday, November 21, 2023 10:34 AM
To: 'ccp4bb' mailto:ccp4bb@jiscmail.ac.uk>>; CCP4 WG1 
mailto:ccp4...@listserv.stfc.ac.uk>>; CCP4 WG2 
mailto:ccp4...@listserv.stfc.ac.uk>>; 
'cc...@jiscmail.ac.uk' mailto:cc...@jiscmail.ac.uk>>; 
'c...@jiscmail.ac.uk' mailto:c...@jiscmail.ac.uk>>; 
'pheni...@phenix-online.org' 
mailto:pheni...@phenix-online.org>>; 
'pdbe-api-us...@ebi.ac.uk' 
mailto:pdbe-api-us...@ebi.ac.uk>>
Subject: RE: CCP4 Study Weekend 2024 - Early bird registration including 
standard student bursary deadline EXTENDED TO FRIDAY 24TH NOVEMBER!
Importance: High

The early bird deadline for in-person registration for the CCP4 Study Weekend 
2024 has been extended until Friday 24th November.

Regards

Karen McIntyre

CCP4 Project Administrator
CCP4 Equality, Diversity and Inclusion Champion
Member of SCD ED Working Group

Science and Technology Facilities Council
karen.mcint...@stfc.ac.uk
Zoom phone: 01235 44 5790

[cid:image001.png@01DA2463.11ADDC60]

**Hours of work: Monday to Thursday: 8.30am to 1.30pm, Friday 10:30am to 
3.30pm.  Please note that I only work part-time **

From: McIntyre, Karen (STFC,RAL,SC)
Sent: Friday, November 17, 2023 12:05 PM
To: 'ccp4bb' mailto:ccp4bb@jiscmail.ac.uk>>; CCP4 WG1 
mailto:ccp4...@listserv.stfc.ac.uk>>; CCP4 WG2 
mailto:ccp4...@listserv.stfc.ac.uk>>; 
'cc...@jiscmail.ac.uk' mailto:cc...@jiscmail.ac.uk>>; 
'c...@jiscmail.ac.uk' mailto:c...@jiscmail.ac.uk>>; 
'pheni...@phenix-online.org' 
mailto:pheni...@phenix-online.org>>; 
'pdbe-api-us...@ebi.ac.uk' 
mailto:pdbe-api-us...@ebi.ac.uk>>
Subject: CCP4 Study Weekend 2024 - Early bird registration including standard 
student bursary deadline ends this SUNDAY!
Importance: High

Dear all,

Registration is open for the 2024 CCP4 study weekend entitled "Decision making 
in MX - how to be a productive structural biologist".

Important Key Dates:
* Early bird registration final date: 19 November 2023;
* We have assisted places available for students registering during early bird 
period i.e. now until 19 November - which cover the cost of registration plus 
one night accommodation meaning students only pay for aqdditional nights 
accommodation @ £63 per night;
* Registration for in-person delegates closes 4 December 2023 (or earlier if 
in-person places sell out although you will be able to join the in-person 
waitlist).

This year we are focusing on decision-making in macromolecular crystallography: 
when to use what automated tool, how to interpret the output and when you need 
to get your hands dirty instead. The frontiers of crystallography now involve 
massive multi-crystal and multi-dimensional experiments. This means the more 
that you can leave to the automated pipelines, the more you can focus on the 
novel elements of your experiment. Sometimes those automated tools work, and 
sometimes they fail (but have maybe not told you exactly why or how). Sometimes 
they don't even exist. In that case, how can you return to the basics and 
develop new strategies to break down the barriers to publication?

Once again, this year the CCP4 Study Weekend will be

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

2023-12-01 Thread Roberto Steiner 
Based however on an AlphaFold version that I guess will be at some point 
released. I was wondering if someone had an early access….
Oh well…I guess we will find out how it performs on ligands soon enough.

Cheers
Roberto


Roberto A Steiner
www.steinerlab.org
https://twitter.com/steiner_lab

roberto.stei...@kcl.ac.uk
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London
Room 3.10A
New Hunt's House, Guy's Campus
SE1 1UL, London, UK
Phone 0044 20 78488216
Fax0044 20 78486435

roberto.stei...@unipd.it
Dipartimento di Scienze Biomediche
Università degli Studi di Padova
Viale G. Colombo 3
35131 Padova, Italia
Telefono 0039 049 8276409

Responses to emails are not expected outside of your normal working hours.








On 1 Dec 2023, at 14:35, Frank von Delft 
mailto:frank.vonde...@cmd.ox.ac.uk>> wrote:

That's a press release, not a tool that can be tested.


On 01/12/2023 12:19, Roberto Steiner wrote:
Great paper indeed!

However quite significant progress seems to have been achieved with ligands as 
well (and not only)…
 
https://deepmind.google/discover/blog/a-glimpse-of-the-next-generation-of-alphafold/
Has anyone in the community put this to the test?


Best wishes
Roberto


Roberto A Steiner
www.steinerlab.org
https://twitter.com/steiner_lab

roberto.stei...@kcl.ac.uk
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London
Room 3.10A
New Hunt's House, Guy's Campus
SE1 1UL, London, UK
Phone 0044 20 78488216
Fax0044 20 78486435

roberto.stei...@unipd.it
Dipartimento di Scienze Biomediche
Università degli Studi di Padova
Viale G. Colombo 3
35131 Padova, Italia
Telefono 0039 049 8276409

Responses to emails are not expected outside of your normal working hours.








On 30 Nov 2023, at 22:35, Tom Terwilliger 
>
 wrote:


You don't often get email from 
b6116340b489-dmarc-requ...@jiscmail.ac.uk.
 Learn why this is important

Hi Structural biologist colleagues!

Our article that helps you make the case that the experiment is still very much 
needed is now out:

https://www.nature.com/articles/s41592-023-02087-4

"AlphaFold predictions are valuable hypotheses and accelerate but do not 
replace experimental structure determination."  Nature Methods (2023)

Also, here is a video on the Phenix Tutorials YouTube channel that describes 
this analysis:  https://www.youtube.com/watch?v=ugMPYdPo8Bc

(I hope you will be happy to see that you and your structural biology 
colleagues get the credit for making AlphaFold possible at 2:35 in the 
introduction of this video!  Keep up the fantastic structural biology work!)

All the best,
Tom T
--
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: 
tterwilli...@newmexicoconsortium.org
Tel: 505-431-0010




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

2023-12-01 Thread Frank von Delft 

That's a press release, not a tool that can be tested.


On 01/12/2023 12:19, Roberto Steiner wrote:

Great paper indeed!

However quite significant progress seems to have been achieved with 
ligands as well (and not only)…

https://deepmind.google/discover/blog/a-glimpse-of-the-next-generation-of-alphafold/
Has anyone in the community put this to the test?


Best wishes
Roberto


*Roberto A Steiner*
www.steinerlab.org 
https://twitter.com/steiner_lab
roberto.stei...@kcl.ac.uk
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London
Room 3.10A
New Hunt's House, Guy's Campus
SE1 1UL, London, UK
Phone 0044 20 78488216
Fax    0044 20 78486435

roberto.stei...@unipd.it
Dipartimento di Scienze Biomediche
Università degli Studi di Padova
Viale G. Colombo 3
35131 Padova, Italia
Telefono 0039 049 8276409

/Responses to emails are not expected outside of your normal working 
hours./









On 30 Nov 2023, at 22:35, Tom Terwilliger 
 wrote:




You don't often get email from 
b6116340b489-dmarc-requ...@jiscmail.ac.uk. Learn why this is 
important 



Hi Structural biologist colleagues!

Our article that helps you make the case that the experiment is still 
very much needed is now out:


https://www.nature.com/articles/s41592-023-02087-4

"AlphaFold predictions are valuable hypotheses and accelerate but do 
not replace experimental structure determination."  Nature Methods (2023)


Also, here is a video on the Phenix Tutorials YouTube channel that 
describes this analysis: https://www.youtube.com/watch?v=ugMPYdPo8Bc


(I hope you will be happy to see that you and your structural biology 
colleagues get the credit for making AlphaFold possible at 2:35 in 
the introduction of this video!  Keep up the fantastic 
structural biology work!)


All the best,
Tom T
--
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilli...@newmexicoconsortium.org
Tel: 505-431-0010




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 








To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 








To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] 2 fully funded PhD studentships in Newcastle University

2023-12-01 Thread Paula Salgado 
Dear colleagues

Just wanted to highlight 2 fully funded PhD studentships in my lab with strong 
structural biology focus - protein crystallography, cryoEM, cryoET and 
combinatorial approaches, combined with biochemistry and microbiology to study 
antibiotic-resistant pathogen C. difficile.

Would really appreciate it if you can share with potential interested 
candidates in your institutions. I'm happy to chat and provide more details and 
support with applications.


  1.
MRC funded - Deadline 17 Dec, on C. difficile sporulation proteins; 
co-supervisor Dr Jamie Blaza, University of York

https://www.findaphd.com/phds/project/stopping-a-superbug-s-sleeping-cells-molecular-machines-of-sporulation-at-atomic-level/?p163517

  
2.  BBSRC funded - Deadline 15 Jan, on C. difficile S-layer; 
co-supervisor Dr Agnieska Bronowska (NU), Dr Karrera Djoko (Durham) and Prof 
Maria Harkiolaki (DLS)
https://www.findaphd.com/phds/project/bbsrc-nld-doctoral-training-partnership-piercing-the-armour-c-difficile-s-layer-permeability/?p165084

Many thanks!


===

Professor Paula S. Salgado
Chair of Structural Microbiology


Due to my own work/life balance, my reply might be delayed and you might get 
emails outside your normal working hours. In any case, I do not expect a 
response outside those hours. Stay safe.


Newcastle University Biosciences Institute
Faculty of Medical Sciences
2nd Floor Cookson Building
Newcastle University
Newcastle upon Tyne, NE2 4HH, UK

Tel: +44 (0)191 208 7432
Email: paula.salg...@ncl.ac.uk





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

2023-12-01 Thread Roberto Steiner 
Great paper indeed!

However quite significant progress seems to have been achieved with ligands as 
well (and not only)…
 
https://deepmind.google/discover/blog/a-glimpse-of-the-next-generation-of-alphafold/
Has anyone in the community put this to the test?


Best wishes
Roberto


Roberto A Steiner
www.steinerlab.org
https://twitter.com/steiner_lab

roberto.stei...@kcl.ac.uk
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London
Room 3.10A
New Hunt's House, Guy's Campus
SE1 1UL, London, UK
Phone 0044 20 78488216
Fax0044 20 78486435

roberto.stei...@unipd.it
Dipartimento di Scienze Biomediche
Università degli Studi di Padova
Viale G. Colombo 3
35131 Padova, Italia
Telefono 0039 049 8276409

Responses to emails are not expected outside of your normal working hours.








On 30 Nov 2023, at 22:35, Tom Terwilliger 
>
 wrote:

You don't often get email from 
b6116340b489-dmarc-requ...@jiscmail.ac.uk.
 Learn why this is important
Hi Structural biologist colleagues!

Our article that helps you make the case that the experiment is still very much 
needed is now out:

https://www.nature.com/articles/s41592-023-02087-4

"AlphaFold predictions are valuable hypotheses and accelerate but do not 
replace experimental structure determination."  Nature Methods (2023)

Also, here is a video on the Phenix Tutorials YouTube channel that describes 
this analysis:  https://www.youtube.com/watch?v=ugMPYdPo8Bc

(I hope you will be happy to see that you and your structural biology 
colleagues get the credit for making AlphaFold possible at 2:35 in the 
introduction of this video!  Keep up the fantastic structural biology work!)

All the best,
Tom T
--
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: 
tterwilli...@newmexicoconsortium.org
Tel: 505-431-0010




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/