Re: [ccp4bb] open review?

[Sweet, Robert]

Dear James,

Indeed, others are thinking about openness in review of academic documents. In 
particular I know of a  group who address particularly the idea that reviews, 
in this case of scientific manuscripts, might be signed by the reviewer. The 
group Biophysics Colab (https://sciety.org/groups/biophysics-colab/about), 
which is a run principally by and for researchers and is supported by eLife, 
are working to accomplish just this. They work to assure frank and open 
discussion that leads to improvement of the paper. They also seek to engage 
knowledgeable reviewers with diverse backgrounds who may ordinarily be 
overlooked by traditional publishers.

I poked around on their lists for a while and found this one, from a year ago; 
it's impressive:
https://sciety.org/articles/activity/10.1101/2021.07.05.451181
One sees a substantial discussion back and forth with three reviewers, and then 
a final version of the paper.

The "Read the full article" link at the top of that page leads one to the 
BioRxiv page of that preprint, https://doi.org/10.1101/2021.07.05.451181, where 
the title box reveals that it was finally published in Nature Communications.

Several published versions of papers acknowledge suggestions from Biophysics 
Colab reviewers by name: 
https://www.nature.com/articles/s41467-022-30300-z#Ack1, and 
https://www.nature.com/articles/s41467-022-30406-4#Ack1.

I've learned that the Biophysics Colab procedure is to assign one of their 
volunteers as a curator to papers they discover in BioRxiv, whose job is to 
interest the author in such a review, and then to recruit reviewers. Their 
organization is in a flexible early stage and they are eager for feedback about 
how to create the best service for the research community. Anyone interested in 
this might reach them at enquir...@sciencecolab.org. Perhaps this effort will 
follow the trajectory implied in this thread towards truly open review.

Yours, Bob

=
  Robert M. Sweet   E-Dress:  sw...@bnl.gov
  Scientific Advisor, CBMS: The Center for BioMolecular
   Structure at NSLS-II
  Photon Sciences, Brookhaven Nat'l Lab.
  Upton, NY  11973 U.S.A.
  Phone:   631 338 7302  (Mobile)
=

From: CCP4 bulletin board  on behalf of John R Helliwell 

Sent: Thursday, June 23, 2022 9:18 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] open review?

Dear James,
This is an interesting question you have posed.

The trend to open peer review reports in articles that we see more often today 
got a major kick off by the ASAPBio Workshop some years back 
https://asapbio.org/peer-review
 . The workshop questions to participants included “would you sign your 
report?”. Earlier career researchers were not in favour due to fear of 
retribution by later career researchers whose submitted articles they would 
have to criticise.

Your question however concerns “open review of research grant proposals?”. 
Different approaches have been tried, most famously perhaps the allocate funds 
randomly via a lottery. In trying to locate the weblink to that I found a more 
comprehensive overview of all sorts of methods and applied to a wide variety of 
types of grant proposals 
https://www.embopress.org/doi/full/10.15252/embr.201949472
Perhaps most interestingly higher risk ie adventurous proposals such as done by 
The Wellcome Trust some years back did not involve peer review at all as 
reviewers couldn’t be trusted to take anything other than a highly critical 
stance. A project manager decided on which got funded.

On reading your message I have also twitter messaged ASAPBio for any further 
info of possible previous workshops that may have addressed open peer review of 
research grant proposals, mentioning your name as the originator of the 
question. If not, a workshop could be convened. (:-)

I once was on an interviewing panel for a UK funder Advanced Fellowship. One 
applicant opened their interview with the statement “I am very sorry to say 
that when I joined a laboratory in country x, the laboratory Head asked to see 
my Advanced Fellowship proposal. He put all the staff in the lab to do the 
investigations. So, unfortunately their are no new ideas remaining.” Similarly 
the developing world’s researchers are very worried about the Global North 
sucking up their data, of all kinds, and doing the analyses that they would 
like to do themselves but more slowly. Open science will need very careful 
implementation. UNESCO are currently giving this a very 

[ccp4bb] System for production of proteins with intrinsically disordered region (IDRs)

[Juliana Ferreira de Oliveira]

Hello!

To those who have experience with the production of human proteins with 
intrinsically disordered region (IDRs), which expression system do you 
recommend? When bacteria doesn´t work...

Mammalian cells, cell-free protein synthesis (CFPS) or any other system?

Thank you!

Best regards,

Juliana Oliveira, PhD
Researcher
LNBio - CNPEM
[cid:image001.png@01D8870D.2F0FD140]



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Re: [ccp4bb] Solubility of Aluminum Fluoride

[Firdous Tarique]

Thanks everyone for their wonderful suggestions.

Best

F

On Wed, Jun 22, 2022 at 11:42 AM Patrick Loll  wrote:

> Kevin and Guillaume said it all quite well. I just want to stress one
> thing, namely that these solutions are metastable, and will eventually
> precipitate (hours to days).
>
> In the case of the beryllium salts, the precipitation is due to slow
> formation of metal hydroxide species. I have no direct experience with the
> aluminum variants, but since aluminum is notorious for forming goopy
> hydroxides, I would guess that the same issue pertains. So make the
> solution right before using, try not to use a pH too far above neutrality,
> and be very cautious about (for example) putting any of these solutions
> into an FPLC.
>
> Pat
>
> > On 22 Jun 2022, at 12:15 PM, Dr. Kevin M Jude 
> wrote:
> >
> > Sorry, I should have said ADPBeF3 (not ADPBeF4), and increase the NaF
> proportion for ADPAlF4. Which in practice means reducing the concentrations
> of everything else due to limited solubility of NaF.
> >
> > From: CCP4 bulletin board  on behalf of Dr.
> Kevin M Jude 
> > Date: Wednesday, June 22, 2022 at 9:10 AM
> > To: CCP4BB@JISCMAIL.AC.UK 
> > Subject: Re: [ccp4bb] Solubility of Aluminum Fluoride
> >
> > I posted the following to ccp4bb in 2017 in response to a similar
> question about ADPBeF4. For AlF4 you’ll increase the NaF stoichiometrically:
> >
> > reagent[stock] (mM)final concentration (mM)volume (µl)
>
> > BeCl2  100090  9
> > NaF750 450 60
> > ADP, pH 8  100 30  30
> > H2O1
> > total volume   100
> >
> > To prepare ADP:Be:F (1:3:15)
> > Prepare BeCl2 stock in the fume hood due to release of Cl2 gas
>
> > thoroughly mix BeCl2 and NaF
> > Add ADP
> > dilute with H2O to final volume
> >
> > This is done at room temperature and the reactions are fast. Careful
> mixing (and adjusting the pH of the ADP beforehand) are important because
> the BeCl2 stock will precipitate at neutral or elevated pH, and the BeFx
> solution is quite acidic.
> >
> >
> >
>
> ---
> Patrick J. Loll, Ph. D.  (he, him, his)
> Professor of Biochemistry & Molecular Biology
> Drexel University College of Medicine
> Room 10-102 New College Building
> 245 N. 15th St., Mailstop 497
> Philadelphia, PA  19102  USA
>
> (215) 762-7706
> pjl...@gmail.com
> pj...@drexel.edu
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
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[ccp4bb] Senior Scientist in Antibody Engineering position available

[Ronnie]

Job Summary

ModeX Therapeutics is seeking a highlytalented and motivated research scientist 
with expertise in the field ofantibody engineering to join our team. The 
candidate will be part of an established multidisciplinary teamadvancing 
discovery efforts on our earlier-stage programs as well as movingnovel 
therapeutic antibodies into clinic. The individual will work in the 
state-of-the-art laboratory and isresponsible for experimental design, 
execution, data analysis, and recordkeeping and presentation.  This is 
anexciting opportunity to be part of a cross-functional team and contribute 
tothe development of cutting-edge biotherapeutics in a fast-paced, 
rapidlygrowing biotech company with a bold vision. 

Company

ModeX Therapeutics, a subsidiary of OPKO Health, is a biotech startup basedin 
Massachusetts dedicated to the concept of modulating multiple diseasetargets 
with innovative multi-targeting strategies. It was founded by Dr. EliasZerhouni 
and Dr. Gary J. Nabel in 2020 with a team of scientists with proventrack record 
from early research to clinical development, regulatory approvals,and 
commercialization. ModeX is pursuing the development of novelimmune-oncology 
therapeutics for cancers and biotherapeutics against infectiousdisease.

Major responsibilities 

·Interact closely and be part ofinterdisciplinary biologics research 
teams to drive the discovery of innovative therapeutic antibodies and 
theoptimization of their biological and biophysical properties.

·Contribute to ModeX’s multi-targetingstrategy through antibody 
discovery campaigns and structure-based antibodydesign. 

·Develop andimplement high-throughput antibody expression and 
purification platforms. Enhanceoptimization of workflows

·Immunogen immunizationstrategy design. Single B cell sorting and/or 
screening technologies.

·Interpret results and present/communicatewith cross-functional 
colleagues for successful execution and completion ofprojects.

·Stayscientifically current and contribute to the implementation of new 
technologyand instrumentation.

·Ensure effective,high-quality, timely and appropriate documentation in 
electronic laboratorynotebooks.

Qualifications

·PhD in biochemistry, structurebiology or other life science 
disciplines with 3+ years of relevant experience antibodyengineering.

·Hands-on experience inantibody generation and optimization (affinity 
modulation, humanization, PTMmitigation, etc.) in an industrial setting with 
strong track record of deliveryof high quality antibodies.

·Expertise in immunology,B cell biology, cloning, next gen. sequencing 
and data analysis. Hands on experiencein hybridoma/B cell cloning, automation, 
Elisa, BLI/SPR, and FACS.

·Knowledge in proteinengineering using direct evolution methods such as 
yeast surface and mammaliandisplay.

·Knowledge in antibodystructure and experience in structure-based 
protein engineering is preferred.

·Computer skills,including large dataset analysis and basic scripting

·Excellent written andoral communication, organization, and data 
analysis skills.  Outstanding troubleshooting and problem-solvingskills.

·Highly adaptable to afast-paced work environment and capable to work 
both independently andcollaboratively within project teams. 

To apply, please send cover letter and CVto ronnie@modextx.com and 
care...@modextx.com




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Re: [ccp4bb] open review?

[John R Helliwell]

Dear James,
This is an interesting question you have posed. 

The trend to open peer review reports in articles that we see more often today 
got a major kick off by the ASAPBio Workshop some years back 
https://asapbio.org/peer-review . The workshop questions to participants 
included “would you sign your report?”. Earlier career researchers were not in 
favour due to fear of retribution by later career researchers whose submitted 
articles they would have to criticise. 

Your question however concerns “open review of research grant proposals?”. 
Different approaches have been tried, most famously perhaps the allocate funds 
randomly via a lottery. In trying to locate the weblink to that I found a more 
comprehensive overview of all sorts of methods and applied to a wide variety of 
types of grant proposals 
https://www.embopress.org/doi/full/10.15252/embr.201949472 
Perhaps most interestingly higher risk ie adventurous proposals such as done by 
The Wellcome Trust some years back did not involve peer review at all as 
reviewers couldn’t be trusted to take anything other than a highly critical 
stance. A project manager decided on which got funded. 

On reading your message I have also twitter messaged ASAPBio for any further 
info of possible previous workshops that may have addressed open peer review of 
research grant proposals, mentioning your name as the originator of the 
question. If not, a workshop could be convened. (:-)

I once was on an interviewing panel for a UK funder Advanced Fellowship. One 
applicant opened their interview with the statement “I am very sorry to say 
that when I joined a laboratory in country x, the laboratory Head asked to see 
my Advanced Fellowship proposal. He put all the staff in the lab to do the 
investigations. So, unfortunately their are no new ideas remaining.” Similarly 
the developing world’s researchers are very worried about the Global North 
sucking up their data, of all kinds, and doing the analyses that they would 
like to do themselves but more slowly. Open science will need very careful 
implementation. UNESCO are currently giving this a very serious go: 
https://www.unesco.org/en/natural-sciences/open-science .

Greetings,
John 

Emeritus Professor John R Helliwell DSc
IUCr Representative to CODATA,
IUCr Representative to UNESCO’s Open Science discussions.




> On 23 Jun 2022, at 02:08, James Holton  wrote:
> 
> Greetings all,
> 
> I'd like to ask a question that I expect might generate some spirited 
> discussion.
> 
> We have seen recently a groundswell of support for openness and transparency 
> in peer review. Not only are pre-prints popular, but we are also seeing 
> reviewer comments getting published along with the papers themselves. 
> Sometimes even signed by the reviewers, who would have traditionally remained 
> anonymous.
> 
> My question is: why don't we also do this for grant proposals?
> 
> I know this is not the norm. However, after thinking about it, why wouldn't 
> we want the process of how funding is awarded in science to be at least as 
> transparent as the process of publishing the results? Not that the current 
> process isn't transparent, but it could be more so. What if applications, and 
> their reviewer comments, were made public? Perhaps after an embargo period?  
> There could be great benefits here. New investigators especially, would have 
> a much clearer picture of format, audience, context and convention. I expect 
> unsuccessful applications might be even more valuable than successful ones. 
> And yet, in reality, those old proposals and especially the comments almost 
> never see the light of day. Monumental amounts of work goes into them, on 
> both sides, but then get tucked away into the darkest corners of our hard 
> drives.
> 
> So, 2nd question is: would you do it? Would you upload your application into 
> the public domain for all to see? What about the reviewer comments? If not, 
> why not?  Afraid people will steal your ideas? Well, once something is 
> public, its pretty clear who got the idea first.
> 
> 3rd question: what if the service were semi-private? and you got to get 
> comments on your proposal before submitting it to your funding agency? Would 
> that be helpful? What if in exchange for that service you had to review 2-3 
> other applications?  Would that be worth it?
> 
> Or, perhaps, I'm being far too naiive about all this. For all I know there 
> are some rules against doing this I'm not aware of.  Either way, I'm 
> interested in what this community thinks. Please share your views!  On- or 
> off-list is fine.
> 
> -James Holton
> MAD Scientist
> 
> 
> 
> 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 

Re: [ccp4bb] Patterson problem

[Catarina Rodrigues]

Hi Roxanne,

Sorry, I should have replied yesterday. CCT389545 is one example of S710.  I 
was just looking at these series structures and decided to ask you if you had 
something for DHX15.

Best regards
Catarina

Dr Catarina Rodrigues | Senior Scientific Officer
Hit Discovery and Structural Design Team | Cancer Research UK Cancer 
Therapeutics Unit and Structural Biology Division
The Institute of Cancer Research | 15 Cotswold Road, Sutton, London, SM2 5NG

Making the discoveries that defeat cancer
[ICR Logo]

From: CCP4 bulletin board  on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: 23 June 2022 11:04
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Patterson problem

CAUTION: This email originated from outside of the ICR. Do not click links or 
open attachments unless you recognize the sender's email address and know the 
content is safe.

Sorted - confusion in the conversion to orthogonal format..
Eleanor



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[ccp4bb] Patterson problem

[Eleanor Dodson]

Sorted - confusion in the conversion to orthogonal format..
Eleanor

>



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Re: [ccp4bb] open review?

[Harmer, Nicholas]

Dear all,

I'd agree with Frank's sentiment. There is a strong risk that it would put 
reviewers in a conflicted position. You only have to look at say the world of 
literature to see that authors very rarely say anything that isn't positive 
about another author's work publicly. As a grant panellist I've already seen 
plenty of reviews that are little more than hagiographies of the great 
professor!

That doesn't mean that James's suggestion is a bad one; it just means that it 
would need a change in the whole ecosystem. Perhaps it is time that funding 
agencies considered hiring professional reviewers, rather than expecting 
academics to do it for free. Professional reviewers would likely gain from 
open, appropriately critical reviews as their reputation would depend on 
delivering reviews that are valid, selective, and high quality. This could 
offer an attractive alternative career for postdocs who have decided not to go 
for academic positions or academics looking for a part-time role as they move 
into retirement.
I would argue that one of the consequences of the pandemic is that academic 
workloads have changed from "unsustainably high" to "completely unsustainable". 
Academia is becoming increasingly non-inclusive as those with caring 
responsibilities, disabilities, and other issues that constrict their time 
cannot keep up with all the "extras" that are expected. Removing the burden of 
reviews from our backs would help bringing back balance.

I suspect that what is needed is proper trials of different approaches, with 
pre-defined criteria for success. Winston Churchill described democracy as "the 
worst form of government - except for all the others that have been tried." I'd 
feel that same about our current peer review system until we have clear 
evidence that there is something better!

Nic

From: CCP4 bulletin board  On Behalf Of Frank von Delft
Sent: 23 June 2022 07:09
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] open review?

I suspect funders will worry about it becoming even harder to find reviewers - 
they're already hard to flush out, if I'm not mistaken, and might become even 
more reclusive if they run the risk of being pilloried in public.

If that sounds theoretical:  even in this community, for all its collegiality 
and friendliness, we pillory one another in public and print just about our 
data.

Frank

On 23/06/2022 02:08, James Holton wrote:
Greetings all,

I'd like to ask a question that I expect might generate some spirited 
discussion.

We have seen recently a groundswell of support for openness and transparency in 
peer review. Not only are pre-prints popular, but we are also seeing reviewer 
comments getting published along with the papers themselves. Sometimes even 
signed by the reviewers, who would have traditionally remained anonymous.

My question is: why don't we also do this for grant proposals?

I know this is not the norm. However, after thinking about it, why wouldn't we 
want the process of how funding is awarded in science to be at least as 
transparent as the process of publishing the results? Not that the current 
process isn't transparent, but it could be more so. What if applications, and 
their reviewer comments, were made public? Perhaps after an embargo period?  
There could be great benefits here. New investigators especially, would have a 
much clearer picture of format, audience, context and convention. I expect 
unsuccessful applications might be even more valuable than successful ones. And 
yet, in reality, those old proposals and especially the comments almost never 
see the light of day. Monumental amounts of work goes into them, on both sides, 
but then get tucked away into the darkest corners of our hard drives.

So, 2nd question is: would you do it? Would you upload your application into 
the public domain for all to see? What about the reviewer comments? If not, why 
not?  Afraid people will steal your ideas? Well, once something is public, its 
pretty clear who got the idea first.

3rd question: what if the service were semi-private? and you got to get 
comments on your proposal before submitting it to your funding agency? Would 
that be helpful? What if in exchange for that service you had to review 2-3 
other applications?  Would that be worth it?

Or, perhaps, I'm being far too naiive about all this. For all I know there are 
some rules against doing this I'm not aware of.  Either way, I'm interested in 
what this community thinks. Please share your views!  On- or off-list is fine.

-James Holton
MAD Scientist



To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] open review?

[Frank von Delft]

I suspect funders will worry about it becoming even harder to find 
reviewers - they're already hard to flush out, if I'm not mistaken, and 
might become even more reclusive if they run the risk of being pilloried 
in public.


If that sounds theoretical:  even in this community, for all its 
collegiality and friendliness, we pillory one another in public and 
print just about our /data/.


Frank


On 23/06/2022 02:08, James Holton wrote:

Greetings all,

I'd like to ask a question that I expect might generate some spirited 
discussion.


We have seen recently a groundswell of support for openness and 
transparency in peer review. Not only are pre-prints popular, but we 
are also seeing reviewer comments getting published along with the 
papers themselves. Sometimes even signed by the reviewers, who would 
have traditionally remained anonymous.


My question is: why don't we also do this for grant proposals?

I know this is not the norm. However, after thinking about it, why 
wouldn't we want the process of how funding is awarded in science to 
be at least as transparent as the process of publishing the results? 
Not that the current process isn't transparent, but it could be more 
so. What if applications, and their reviewer comments, were made 
public? Perhaps after an embargo period? There could be great benefits 
here. New investigators especially, would have a much clearer picture 
of format, audience, context and convention. I expect unsuccessful 
applications might be even more valuable than successful ones. And 
yet, in reality, those old proposals and especially the comments 
almost never see the light of day. Monumental amounts of work goes 
into them, on both sides, but then get tucked away into the darkest 
corners of our hard drives.


So, 2nd question is: would you do it? Would you upload your 
application into the public domain for all to see? What about the 
reviewer comments? If not, why not?  Afraid people will steal your 
ideas? Well, once something is public, its pretty clear who got the 
idea first.


3rd question: what if the service were semi-private? and you got to 
get comments on your proposal before submitting it to your funding 
agency? Would that be helpful? What if in exchange for that service 
you had to review 2-3 other applications?  Would that be worth it?


Or, perhaps, I'm being far too naiive about all this. For all I know 
there are some rules against doing this I'm not aware of. Either way, 
I'm interested in what this community thinks. Please share your 
views!  On- or off-list is fine.


-James Holton
MAD Scientist



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