[ccp4bb] Funded PhD position near Paris, France: AI-powered prediction of protein-nucleic acid interactions

[ANDREANI Jessica]

Dear all,

please find below an announcement for a funded PhD position on the development 
of deep learning approaches to predict interactions between proteins and 
nucleic acids. The deadline for application is 30 April 2023.

Best regards,
Jessica Andreani

Scientific project
Interactions between proteins and nucleic acids have strong biological 
relevance and are often perturbed in diseases. This project aims to better 
understand the molecular mechanisms of protein-nucleic acid interactions. A 
large gap exists between vast amounts of high-throughput protein-nucleic acid 
interaction data and the scarcity of 3D structures of protein-nucleic acid 
complexes, triggering the need for computational methods to analyze and predict 
these structures. Recently, artificial intelligence (in particular deep 
learning in AlphaFold and related methods) has emerged as a revolutionary 
approach to predict protein and protein-protein interaction structures.
The present project aims to develop computational approaches for the analysis 
and prediction of protein-nucleic acid interactions, by building upon deep 
learning methodologies and integrating complementary data sources. We will also 
use an evolutionary perspective to provide crucial insights into the exquisite 
regulation of complex processes driven by protein-nucleic acid interactions.

Host team and environment for the PhD project
The doctoral research will take place in the “Molecular assemblies and genome 
integrity” team of I2BC (Institute for Integrative Biology of the Cell, UMR 
9198 CEA/CNRS/Université Paris-Saclay). I2BC is a research institute of 
Université Paris-Saclay that gathers 60 research teams covering a wide range of 
integrative biology projects. The “Molecular assemblies and genome integrity” 
team relies on a strong coupling between computational and experimental 
approaches to characterize, predict and inhibit macromolecular interactions. 
I2BC is localized in Gif sur Yvette (less than one hour from the center of 
Paris).
Our bioinformatics team has a strong expertise in macromolecular structure and 
evolution, macromolecular interaction prediction and heterogeneous data 
integration. In recent years, our team developed original approaches for the 
structural prediction of protein interactions using evolutionary information 
(Quignot et al, NAR 2021; Quignot et al, Bioinformatics 2021). We also have 
numerous collaborations with wet-lab biologists. We have access to relevant 
computational resources, including GPU cluster nodes.

Funding and benefits
CEA will provide 3 years PhD funding for this project to an excellent PhD 
candidate. The gross monthly salary for CEA doctoral students is €2,290 (as of 
October 2022). CEA doctoral students have access to the same benefits as other 
CEA employees (social security contributions, training opportunities, company 
canteen, paid leave, social benefits…). Expected start of the PhD position: 
October 2023.

Expected profile
We are looking for a highly motivated candidate with a Master's degree in 
bioinformatics, data science, machine learning or a related field. Proficiency 
in Python programming is necessary. Previous experience in deep learning and 
data science is highly desirable. (Structural) bioinformatics experience is a 
plus but not strictly required, provided the candidate has a strong interest in 
life sciences and molecular aspects.

Application process
Please send a CV, a motivation letter and contact details of two references 
(ideally, researchers who have supervised the candidate for relevant research 
projects) to Jessica Andreani: 
jessica.andre...@cea.fr
Deadline for application: 30 April 2023




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[ccp4bb] refmac output query

[Emmanuel Saridakis]

Dear All,

A quick question about Refmac on ccp4i. When refining an RNA oligonucleotide 
structure using the findwaters option, the pdb output labels all the atoms as 
HETATM (inluding the original RNA atoms which were not so labelled in the input 
pdb). It is of course trivial to correct this, but I was wondering if there is 
a hidden problem somewhere, that might influence more crucial things.

Many thanks,
Emmanuel

-- 
Dr. Emmanuel Saridakis
Institute of Nanoscience and Nanotechnology
National Centre for Scientific Research "DEMOKRITOS"
15310 Athens
GREECE



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Re: [ccp4bb] Covalent link with AceDRG

[Rob Nicholls]

Dear Marian,

How do you know that it’s still a double bond? Is it due to the way that it’s 
displayed in Coot, or based on the interatomic distances after refinement?

Could you have a look in the AceDRG link dictionary (.cif) and confirm the 
order of the bond? Search for a “_chem_mod_bond” loop (there will be two of 
these - one for each of the linked compounds), and you should see that the 
relevant bond is there and listed as “single”, with an appropriate target 
value. Is that what you see?

Regards,
Rob


> On 16 Mar 2023, at 11:09, Marian Oliva  wrote:
> 
> 
> CAUTION: This email originated from outside of the LMB.
> Do not click links or open attachments unless you recognize the sender and 
> know the content is safe.
> .-owner-ccp...@jiscmail.ac.uk-.
> Dear all,
> 
> I'm having an issue running AceDRG for making a covalent link between a 
> compound (with a double bond) and a target His (linking atom NE2). 
> 
> I am running the program in ccp4i2 (ccp4-7.1.018). I have, of course, include 
> the .cif file of the compound (obtained from SMILE using eLBOW) and specify 
> the atom I want to link with the His. As this atom is involved in a double 
> bond I also specify to change the order of bond between this atom and the 
> next one into single. Finally, I set that the order of bond between linking 
> atoms is single.
> 
> The program run and the link is stablished between the atom of the compound 
> and the His NE2 BUT, the double bond within the compound is still there. 
> 
> I’m not sure what can be happening and any help will be really appreciated.
> 
> Best,
> Marian 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 



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[ccp4bb] Covalent link with AceDRG

[Marian Oliva]

Dear all,

I'm having an issue running AceDRG for making a covalent link between a 
compound (with a double bond) and a target His (linking atom NE2). 

I am running the program in ccp4i2 (ccp4-7.1.018). I have, of course, include 
the .cif file of the compound (obtained from SMILE using eLBOW) and specify the 
atom I want to link with the His. As this atom is involved in a double bond I 
also specify to change the order of bond between this atom and the next one 
into single. Finally, I set that the order of bond between linking atoms is 
single.

The program run and the link is stablished between the atom of the compound and 
the His NE2 BUT, the double bond within the compound is still there. 

I’m not sure what can be happening and any help will be really appreciated.

Best,
Marian 


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[ccp4bb] Postdoctoral Fellow for Synchrotron MX Data Acquisition and Analysis

[Leonarski Filip]

Dear Colleagues from the CCP4bb,

Paul Scherer Institute in Switzerland is hiring a postdoctoral fellow for a 
project to develop a NextGen Detector Control Unit. The project is realized 
together with DECTRIS, leading manufacturer of hybrid pixel X-ray detectors, 
and supported by Innosuisse (Swiss Agency for Innovation).

We are looking for a candidate with a PhD in biology, chemistry, physics, 
geology, computing or related fields and a track record in analyzing large 
experimental or simulated datasets. Good programming skills in Python are 
essential.

We are looking for a candidate with a curiosity to learn accelerated computing 
(FPGA, GPU) and machine learning methods, but no prior experience in these 
fields is necessary.

More information can be found on PSI web site:
https://www.psi.ch/en/pa/job-opportunities/56419-postdoctoral-fellow

Please submit your application online by 25 April 2023.

Please feel free to contact me directly with any questions.

With best regards,
Filip

--

Dr Filip Leonarski
Beamline Data Scientist
Swiss Light Source
Paul Scherrer Institut
tel: +41 56 310 5652



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[ccp4bb] Call for beamtime proposals at Diamond Light Source. Deadline 1700 29th March 2023

[Hall, Dave (DLSLtd,RAL,LSCI)]

Dear All

The call for proposals via peer-review for non-proprietary access to Diamond MX 
beamlines from October 2023 until March 2024 is now open 
(https://www.diamond.ac.uk/Users/Apply-for-Beamtime.html). The deadline for 
this call is Wednesday 29th March at 17:00 hrs UTC+1/GMT+1.

Diamond Light Source, the UK’s national synchrotron, provides access for users 
worldwide to a suite of seven MX 
beamlines. The beamlines cover a 
very broad range of capabilities including:

  *   high throughput (I03, 
I04, 
I04-1, 
I24, 
VMXi)
  *   micro (I04, 
I24, 
VMXi, 
VMXm) and nano-focus 
(VXMm) beams
  *   extremely long wavelengths 
(I23)
  *   room temperature in situ collection from crystallisation plates 
(VMXi)
  *   (time resolved) serial synchrotron crystallography 
(I24, 
VMXi)
  *   the fragment-based screening platform 
(XChem)
  *   additionally the suite can handle biological agents up to Hazard Group 3

Experiment sessions on the beamlines are via responsive 
scheduling,
 pre-scheduled visits (either remote or on-site) and automated unattended data 
collection.

The route for access through this call to I03, I04, I04-1, I23, I24, VMXi and 
the XChem facility is either via a Block Allocation 
Group or 
standard 
access 
proposal.

The nano-focus beamline VMXm is currently accessible via a user commissioning 
call – please contact Gwyndaf Evans for more details.

Additionally, as part of iNEXT-Discovery (https://inext-discovery.eu/ & 
https://www.diamond.ac.uk/Users/Support-for-European-Access-to-Life-Sciences/iNEXT-Discovery---access-to-Diamond.html)
 we are supporting access for European based research groups to the following 
modalities within the MX group at Diamond. Before applying directly to 
iNEXT-Discovery please do touch base with the following for advice:


  *   Serial Crystallography @I24 – Robin Owen
  *   Serial Crystallography @VMXi – Mike Hough
  *   Long Wavelength @I23 – Armin Wagner
  *   Micro/nanofocus crystallography @VMXm – Gwyndaf Evans
  *   Drug discovery: Fragment screening – Frank von Delft

If you have any queries on particular beamline capabilities or techniques 
please contact the relevant principal beamline scientist or myself.

Best regards

Dave Hall on behalf of the MX group at Diamond.
--
MX Group
Diamond Light Source
Didcot
United Kingdom
OX11 0DE
https://www.diamond.ac.uk/Instruments/Mx.html


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Re: [ccp4bb] anomalous data usage

[Paul Bond]

I believe there are many advantages to storing things *internally* as data
objects with metadata instead of as columns of an MTZ file. How many
students know what FP,SIGFP mean? And how many know that the FP,SIGFP
columns in Refmac's HKLIN are not the same as the FP,SIGFP columns in
HKLOUT? In an interface you can give these much more friendly names such as
"observed amplitudes" and "amplitudes scaled by Refmac". The problem is
that people should not need to access the *internal *i2 files to get to
this data. Currently, you can export mini MTZs (containing only one data
object) at the bottom of each report and you can export a full MTZ from
Refmac using the Export MTZ button at the top of the interface, but
probably this issue can be solved by doing the following:

   1. Making sure that reflection data objects have sensible names
   2. Expanding the "Export MTZ" functionality to have a customisable
   selection of any data objects (and allowing customisation of column labels
   as there may be clashes)

Kind regards,
Paul

On Thu, 16 Mar 2023 at 07:14, Jan Dohnalek  wrote:

> We are hitting the same problems also with students (so no rigidified
> brains I think) ... the concept of "files" seems absolutely natural (also
> to them) and when they ask about solving more tricky problems in i2 ... we
> do the obvious, go back to ccp4i.
>
> I2 is fine when things are smooth and easy.
>
> Jan
>
>
> On Wed, Mar 15, 2023 at 3:52 PM Randy John Read  wrote:
>
>> Hi Jon,
>>
>> My understanding of the philosophy is that new users would prefer to
>> think about crystallographic data objects, rather than worrying about the
>> arcana of MTZ files and the many different flavours of columns. There are
>> tradeoffs — it can indeed be more difficult to find the bits of information
>> you need, but you should be thinking in terms of the stored objects from
>> the imports at the beginning of the project, rather than the files that
>> hold them.
>>
>> Personally, I find multicolumn MTZ files easier to think about, but my
>> brain probably rigidified a decade or two ago!
>>
>> Best wishes,
>>
>> Randy
>>
>> > On 15 Mar 2023, at 13:09, Jon Cooper <
>> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>> >
>> > Hello Ian,
>> >
>> > if I understand you and Eleanor correctly, this is the philosophy of
>> the mini-MTZ, i.e. if you are doing anything independent of i2, you have to
>> dig around a bit to find which output file contains the columns you need.
>> >
>> > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>> >
>> > Sent from Proton Mail mobile
>> >
>> >
>> >
>> >  Original Message 
>> > On 13 Mar 2023, 23:27, Ian Tickle < ianj...@gmail.com> wrote:
>> >
>> >
>> > Eleanor, which program is doing that and more to the point, why?
>> >
>> > -- Ian
>> >
>> >
>> > On Mon, 13 Mar 2023 at 20:17, Eleanor Dodson 
>> wrote:
>> > fIf you are using ccp4I2 for some forgotten reason the final output has
>> one reflection with I+ and I-, another with Imean, another with Fmean -
>> aagghh
>> >
>> >
>> > On Mon, 13 Mar 2023 at 19:40, Ian Tickle  wrote:
>> >
>> > Hi Gottfried
>> >
>> > AIMLESS definitely outputs IMEAN (and SIGIMEAN) by default.
>> >
>> > Cheers
>> >
>> > -- Ian
>> >
>> >
>> > On Mon, 13 Mar 2023 at 18:53, Palm, Gottfried 
>> wrote:
>> > Dear all,
>> >   I have a few questions handling (non) anomalous data:
>> > By default aimless seems to produce Iplus and Iminus columns. Can I
>> force it to (also) create an Imean column?
>> > What does refmac do, when it gets Iplus and Iminus (and their sigmas)
>> as input. Does it take only one of them or does it calculate and use Imean?
>> > Greetings
>> >   Gottfried
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> >
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> >
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> >
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>> >
>>
>> -
>> Randy J. Read
>> Department of Haematology, University of Cambridge
>> Cambridge Institute for Medical Research Tel: +44 1223 336500
>> The Keith Peters Building
>> Hills Road   E-mail:
>> rj...@cam.ac.uk
>> Cambridge CB2 0XY, U.K.
>> www-structmed.cimr.cam.ac.uk
>>
>>
>> 
>>
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>>
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>> available at https://www.jiscmail.a

Re: [ccp4bb] anomalous data usage

[Jan Dohnalek]

We are hitting the same problems also with students (so no rigidified
brains I think) ... the concept of "files" seems absolutely natural (also
to them) and when they ask about solving more tricky problems in i2 ... we
do the obvious, go back to ccp4i.

I2 is fine when things are smooth and easy.

Jan


On Wed, Mar 15, 2023 at 3:52 PM Randy John Read  wrote:

> Hi Jon,
>
> My understanding of the philosophy is that new users would prefer to think
> about crystallographic data objects, rather than worrying about the arcana
> of MTZ files and the many different flavours of columns. There are
> tradeoffs — it can indeed be more difficult to find the bits of information
> you need, but you should be thinking in terms of the stored objects from
> the imports at the beginning of the project, rather than the files that
> hold them.
>
> Personally, I find multicolumn MTZ files easier to think about, but my
> brain probably rigidified a decade or two ago!
>
> Best wishes,
>
> Randy
>
> > On 15 Mar 2023, at 13:09, Jon Cooper <
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> > Hello Ian,
> >
> > if I understand you and Eleanor correctly, this is the philosophy of the
> mini-MTZ, i.e. if you are doing anything independent of i2, you have to dig
> around a bit to find which output file contains the columns you need.
> >
> > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
> >
> > Sent from Proton Mail mobile
> >
> >
> >
> >  Original Message 
> > On 13 Mar 2023, 23:27, Ian Tickle < ianj...@gmail.com> wrote:
> >
> >
> > Eleanor, which program is doing that and more to the point, why?
> >
> > -- Ian
> >
> >
> > On Mon, 13 Mar 2023 at 20:17, Eleanor Dodson 
> wrote:
> > fIf you are using ccp4I2 for some forgotten reason the final output has
> one reflection with I+ and I-, another with Imean, another with Fmean -
> aagghh
> >
> >
> > On Mon, 13 Mar 2023 at 19:40, Ian Tickle  wrote:
> >
> > Hi Gottfried
> >
> > AIMLESS definitely outputs IMEAN (and SIGIMEAN) by default.
> >
> > Cheers
> >
> > -- Ian
> >
> >
> > On Mon, 13 Mar 2023 at 18:53, Palm, Gottfried 
> wrote:
> > Dear all,
> >   I have a few questions handling (non) anomalous data:
> > By default aimless seems to produce Iplus and Iminus columns. Can I
> force it to (also) create an Imean column?
> > What does refmac do, when it gets Iplus and Iminus (and their sigmas) as
> input. Does it take only one of them or does it calculate and use Imean?
> > Greetings
> >   Gottfried
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
>
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> The Keith Peters Building
> Hills Road   E-mail:
> rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
>
> 
>
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>
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> available at https://www.jiscmail.ac.uk/policyandsecurity/
>


-- 
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
Prumyslova 595
252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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