Re: [ccp4bb] AW: [ccp4bb] COOT RSR

[Norbert Straeter]

Dear Paul,

with "dummy water" I refer to a water molecule, which I place at the center of 
a (usually positive) difference electron density peak to be able to measure the 
distances to the environment and decide, what the density actually might be. I 
do that quite often. It could also be any other atom, of course.

Best wishes,

Norbert



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[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] COOT RSR

[Schreuder, Herman /DE]

Hi Paul,

For me, dummy waters are waters placed in very early models, where it is not 
yet clear whether the density belongs to a water, a rearranged side chain or a 
ligand. In the course of the refinement process, it becomes clear to which 
category the density really belongs. Especially for larger rebuilding, I find 
it helpful to use such waters.

A real water is for me a nicely defined, hydrogen bonded water in a 
well-refined structure. However, in this stage one does not need any RSR 
anymore.

Best regards,
Herman

Von: CCP4 bulletin board  Im Auftrag von Paul Emsley
Gesendet: Montag, 22. November 2021 22:09
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] COOT RSR




What's the difference between a dummy water and a real one?

Paul


On 22/11/2021 14:34, Schreuder, Herman /DE wrote:
Dear Paul,

I agree with Oliver and Norbert, in the early phases of refinement, when a lot 
of rebuilding has to be done, the coot RSR is not very helpful and in general I 
leave it to buster do refine the rebuilt regions. Knowing now that (dummy) 
waters may be the culprit, I will remove them. However, it would be much more 
convenient if the  repulsions with water molecules would not be taken into 
account.

Thank you,
Herman

Von: CCP4 bulletin board  
Im Auftrag von Norbert Straeter
Gesendet: Sonntag, 21. November 2021 12:24
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] COOT RSR

Dear Paul,

I agree to Oliver. In situations where you want to fit a "dummy water" to a 
difference density peak (to determine distances to the environment) or try the 
fit of solvent molecules to yet unexplained density, it would be nice to first 
obtain an optimal fit and next think about the environment and possible bumps 
and partial occupancy. I had this problem already several times, that I could 
not get a good fit because of the model repulsions. Even if two partially 
occupied waters are at closed distance the repulsions appear to be active in 
RSR. It is not about the old method being better.

Best wishes,

Norbert



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[ccp4bb] Registration for CCP4 Study Weekend 2022 - EARLY BIRD FOR IN-PERSON DELEGATES STILL OPEN

[Karen McIntyre - STFC UKRI]

We now have 160 delegates coming to the in-person part of the CCP4 Study 
Weekend 2022.

As we still have space for another 60 people max (at 1m+ social distancing - UK 
based delegates only), we have extended the early bird prices for the Study 
Weekend until in-person registrations close on 30th November.

This means that there are still FREE student bursary spaces available - 
Students get their registration fee plus 2 nights accommodation in halls paid.

It also means that the price for standard delegates has not increased.

Come and network with other crystallographers and interact with our in-person 
speakers.

Confirmed in-person speakers include:
Jon Agirre (University of York)
Paul Bond (University of York)
Gerard Bricogne (Global Phasing Ltd)
Lucrezia Catapano (King's College London)
Kevin Cowtan (University of York)
Tristan Croll (University of Cambridge)
Eleanor Dodson (University of York)
Elspeth Garman (Oxford University)
Helen Ginn (Diamond Light Source)
John Helliwell (University of Manchester)
Gerard Kleywegt (EMBL-EBI)
Eugene Krissinel (UKRI-STFC CCP4)
Andrey Lebedev (UKRI-STFC CCP4)
Airlie McCoy (University of Cambridge)
Filomeno Sanchez Rodriguez (University of Liverpool)
Keitaro Yamashita (MRC-LMB)

If you would rather attend the event virtually, please register for the virtual 
event where you will be able to experience the talks.

All the links for registering and more information are below.

Regards

Karen McIntyre

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

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

[cid:image001.png@01D7E073.6DB55460]

**Please note that I only work mornings until 1.30pm**

In line with current government and PHE advise, the SCD admin team are 
currently working remotely.  Please note that due to additional tasks related 
to Covid-19, child-caring responsibilities and a reduced number of staff, there 
might be delays  in our responsiveness, especially for internal non-urgent 
queries and requests.  We thank you in advance for your understanding during 
this uncertain time.

From: McIntyre, Karen (STFC,RAL,SC)
Sent: 17 November 2021 14:27
To: CCP4 WG1 ; CCP4BB@JISCMAIL.AC.UK; CCP4 WG2 
; cc...@jiscmail.ac.uk
Subject: RE: Registration for CCP4 Study Weekend 2022 - EARLY BIRD FOR 
IN-PERSON DELEGATES CLOSES THIS SUNDAY 21st NOVEMBER 2021

Registration is open for the 2022 CCP4 study weekend https://cvent.me/YPqVd0

The topic this year is "Current trends in macromolecular model refinement and 
validation".

***Please note Early Bird registration closes on Sunday 21 November 2021.  Free 
student bursaries for the in-person event end after this point and registration 
fees for standard delegates increase by £50***

This year the meeting will be a hybrid meeting from 5th - 7th January 2022 with 
the in-person event held at East Midlands Conference Centre, Nottingham.

Due to Covid we have had to make a few changes to the event.  We are limiting 
in-person attendance to UK-based delegates only and we only have 220 spaces for 
in-person delegates due to social distancing - overseas delegates (and any 
UK-based delegates that either cannot get an in-person space or do not wish to 
attend in-person) may attend the meeting virtually and we have an unlimited 
number of virtual spaces.  More information on Covid mitigating measures can be 
found at https://cvent.me/014qX1?rt=yPnj__NRIE-gApg49Vlk0w .

A preliminary programme, registration details, and further information can be 
found at the above link.

Confirmed in-person speakers include:
Jon Agirre (University of York)
Paul Bond (University of York)
Gerard Bricogne (Global Phasing Ltd)
Lucrezia Catapano (King's College London)
Kevin Cowtan (University of York)
Tristan Croll (University of Cambridge)
Eleanor Dodson (University of York)
Elspeth Garman (Oxford University)
Helen Ginn (Diamond Light Source)
John Helliwell (University of Manchester)
Gerard Kleywegt (EMBL-EBI)
Eugene Krissinel (UKRI-STFC CCP4)
Andrey Lebedev (UKRI-STFC CCP4)
Airlie McCoy (University of Cambridge)
Filomeno Sanchez Rodriguez (University of Liverpool)
Keitaro Yamashita (MRC-LMB)

Confirmed virtual speakers include:
Pavel Afonine (Lawrence Berkley National Laboratory, USA)
David Armstrong (EMBL-EBI)
Grzegorz Chojnowski (EMBL Hamburg)
Dennis Della Corte (Brigham Young University, USA)
Elke de Zitter (Institut de Biologie Structurale, France)
Paul Emsley (MRC-LMB)
Marcus Fischer (St. Jude Children's Research Hospital, USA)
Lukas Gajdos (Institut Laue-Langevin, France)
Robbie Joosten (NKI, NETHERLANDS)
Oleg Kovalevskiy (UKRI-STFC CCP4)
Victor Lamzin
Dorothee Liebschner (Lawrence Berkley National Laboratory, USA)
Nigel Moriarty (Lawrence Berkley National Laboratory, USA)
Nick Pearce (Vrije Universiteit Amsterdam, NETHERLANDS)
Jane Richardson (Duke University, USA)
Bernhard Rupp
Bohdan Schneider (Institute o

[ccp4bb] [Job openings] Two ML scientist positions at Sanofi on Antibody design & engineering

[Qiu, Yu /US]

Sanofi is one of the top pharmaceutical companies with more than 100,000 people 
in 100 countries. We recently built a multidisciplinary team focusing on using 
ML- and physics-based methods to accelerate design and engineering novel 
protein therapeutics.
https://sanofi.wd3.myworkdayjobs.com/SanofiCareers/job/Framingham-MA/Senior-Data-Scientist--Machine-Learning-for-Biologics_R2617876-1
https://sanofi.wd3.myworkdayjobs.com/SanofiCareers/job/Framingham-MA/Data-Scientist--Machine-Learning-for-Biologics_R2617878-1





Overview:
At Sanofi Large Molecule Research Platform, we have a strong ambition to 
utilize machine learning (ML) and artificial intelligence (AI) in all aspects 
in biologics discovery and development, with comprehensive programs spanning 
from deep repertoire mining to de novo design. Additionally, we are open and 
actively collaborate with leading biotech and academia. The new opening senior 
data scientist role is to seek a machine learning expert with strong expertise 
in modern data analysis methods, including NLP, graph, and 3D geometry-aware 
models. The successful candidate will work in an interdisciplinary team to 
apply cutting-edge computation, ML/DL, sequence-based and structure-based 
methods to resolve challenges in real-world drug discovery. This is an exciting 
opportunity to contribute to the process of design and engineering 
revolutionary biologics, including multivalent, multi-targeting molecules by 
leveraging large amount of proprietary data coming from our industry-leading 
high-throughput automation platforms. The successful candidate will gain deeper 
insight into drug development process and transform ML/DL algorithms into 
accelerating biologics discovery and development process, and make impacts to 
patients’ life.
Your responsibilities include:

  *   Evaluate and develop state-of-the-art computational methods to decode 
biophysical and geometrical features from antibody-antigen datasets and create 
predictive models for engineering.
  *   Develop and apply complex machine/deep learning solutions to our 
high-content and high-quality proprietary datasets, as well as public datasets.
  *   Perform data querying and feature extraction to improve current workflow 
for antibody/nanobody engineering, including affinity modification, 
cross-reactivity engineering, liability risk prediction and mitigation, 
multi-specific antibody engineering, and de novo antibody design.
  *   Maintain a keen awareness of recent developments in data science, 
bioinformatics, and state-of-the-art of ML/DL algorithms, aiming to accelerate 
development of new computational algorithms.
  *   Effectively collaborate with colleagues with diverse scientific 
background, identify problems and opportunities, combine computational and 
structural analysis to support large molecule projects.
Basic qualifications:

  *   Ph. D. in related field such as Biostatistics, Physics, Computation 
Biology, Biomedical Engineering, Computer Science, Applied Mathematics, 
Structural Biology with at least 2 years of experience or Master with at least 
5 years of relevant experience.
  *   Significant depth of expertise in ML/DL, hands-on experience with modern 
machine learning models, including Transformers, Graph NN, Recurrent NN, MLP 
etc.
  *   Sufficient in programing using deep learning libraries such as PyTorch, 
TensorFlow, and Keras. Experience with cloud computing, parallel computing, 
and/or supercomputing is expected.
  *   Track record of applying machine learning/ deep learning approaches to 
solve molecule-related problems. Familiarity with protein structure or sequence 
featurization and learned embeddings.
  *   Experience with database mining, big data, and large-scale virtual 
screening using Bayesian Optimization or Gaussian Processes is desired.
  *   Familiarity with Data Visualization tools/libraries and dimensionality 
reduction algorithms.
Preferred qualifications:

  *   Understanding of protein structure and protein-protein interaction. 
Experience with structural analysis and optimization of biochemical and 
biophysical properties, like thermodynamics, with protein design tools e.g. 
Rosetta, BioLuminate, or MOE, etc.
  *   Understanding of biologics R&D process is a plus.


Yu Qiu
Lab Head, Protein Engineering, Large Molecule Research
Digital Biologics Advanced Applications Lead, Digital Biologics Platform (DBxP)
Sanofi
yu@sanofi.com
TEL.: 508-270-2555
3465 - 49 NEW YORK AVENUE - FRAMINGHAM – Massachusetts 01701
[cidimage003.jpg@01D7DF83.1A470210]

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[ccp4bb] Post-doctoral Positions at St Jude Children's Research Hospital

[Cupido, Tommaso]

Dear All,

The Cupido lab in the Department of Chemical Biology & Therapeutics at St Jude 
Children Research Hospital (Memphis, TN) is seeking postdoctoral fellows who 
wish to conduct structural and chemical biology research and gain experience as 
independent researchers. These positions are core funded.

Candidates should have expertise in biochemistry and structural biology. 
Bioinformatic experience in genomic data analysis is preferred. Successful 
applicants are expected to lead projects, gain multidisciplinary training in 
cutting edge structural and molecular technologies, and eventually open new 
lines of scientific inquiry into outstanding biological problems in chromatin 
and chemical biology. Enthusiasm in integrating different experimental 
approaches is valuable, and postdocs will be encouraged to take full advantage 
of the outstanding scientific technology platforms at St Jude, which include 
dedicated centers for Cryo-EM, biomolecular NMR, super-resolution microscopy, 
high-throughput chemical screening, genomics and proteomics.

About The Lab
The Cupido lab opened on January 2021. Research in the lab focuses on 
discovering drug-like chemical modulators for protein machines and for the 
analysis of molecular mechanisms that control the flow of genetic information 
(i.e. gene transcription and mRNA splicing). Our efforts are highly 
multidisciplinary, integrating small molecule chemistry with structural and 
genomic approaches. One major focus is to understand the precise mechanism and 
regulation of nucleic acid-interacting ATPases whose aberrant function is 
implicated in cancer development. We seek to control the dynamics of these 
protein machines using small molecules we design, identify new pharmacological 
approaches, and test hypotheses for the development of novel cancer 
therapeutics.

The lab is equipped with brand new biochemistry and chemical biology equipment 
and has full access to unparalleled research resources and expertise in an open 
and collaborative environment at St Jude.
Apply here 
https://postdoc-stjude.icims.com/jobs/8803/postdoctoral-research-assoc/job, or 
please send a cover letter emphasizing research background relevant to our area 
of interest and career goals, and a CV to 
tommaso.cup...@stjude.org.




Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer



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[ccp4bb] 2021 Moonshot Webinar - 16 Dec 4pm GMT

[Frank von Delft]

Dear BB

It's been 20 months since we broadcast on this BB (and elsewhere) for 
help to develop a SARS-CoV-2 Mpro inhibitor from XChem fragments.  The 
thing is still going strong, and in the open, with funding up to clinic.


Please do sign up if you're interested in drug discovery and 
development, for a real-time in-depth look at how it's going.


Frank



 




 Hi Frank,


As we approach year end, the Moonshot team would love the chance to 
update you on our 2021 progress and 2022 plans in moving our 
open-science antiviral candidates closer to the clinic.


Come join us for our end of year webinar!

*Details*

 * Date: Thursday 16th December
 * Time: 4pm - 5:30pm GMT

Webinar Registration 
 




If you have any further questions, please reach out to _covid@postera.ai_


Looking forward to seeing you all,
PostEra, on behalf of the COVID Moonshot team



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[ccp4bb] Reminder - Tenure Track Assistant Professor

[Martin Lawrence]

Dear CCP4 Community,

Montana State University (MSU) invites applications for a tenure-track
faculty position in cryogenic electron microscopy.  The position is
formally a joint appointment between the Department of Chemistry and
Biochemistry, and the Department of Microbiology and Cell Biology.  The
candidate will join an active structural biology group with existing
expertise in X-ray crystallography, NMR and mass spectrometry, and developing
expertise in cryo-EM.  The position will include access to the University’s
newly acquired Talos Arctica microscope (MSU Cryo-EM
) equipped with a Gatan
K3 camera capable of high resolution single particle analysis (For example: Mol
Cell 2019 74(1):132
).
The campus also has interests in cryo-ET  (Structure 2019 27(11):1634

 ) and helical reconstruction.  Potential applicants with expertise in any
of these areas are encouraged to apply.  Experience in micro-ED and
macromolecular crystallography are a plus.  *Review of applications will
begin December 1st* and continue until the position is filled.

Montana State University maintains a highly collaborative,
interdisciplinary environment with research programs broadly focused in
multiple areas, including  cell and developmental biology,
neurobiology/neuroscience, metalloproteins and metals in biology, innate
and acquired immunity, virology, pathogen microbiology, host/pathogen
interactions, microbial biofilms and environmental microbiology.  There are
numerous opportunities for collaborations in these areas.

We are located in the Northern Rocky Mountain community of Bozeman
Montana.  Bozeman is regularly recognized for its high quality of life,
including its outdoor, cultural and educational amenities:
http://www.montana.edu/about-msu/bozeman/
.

For further details and to apply, visit:
https://jobs.montana.edu/postings/26344

For inquiries and additional questions, please contact:

Martin Lawrence
lawre...@montana.edu

Martin Lawrence
Professor of Chemistry and Biochemistry
Montana State University
Bozeman, MT 59717



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