[ccp4bb] Multiple Positions available UK

[Panne, Daniel (Prof.)]

Dear all,

We currently have several positions open at different levels! The project is 
part of an interdisciplinary, collaborative and international project involving 
groups in Imperial College London, the Netherlands Cancer Institute (NKI) 
Amsterdam, the University of Oxford, and the University of Leicester.

This project focuses on understanding molecular mechanisms that control the 
regulation of 3D genome organisation. The 3D genome organization refers to the 
spatial arrangement of chromatin within the nucleus, including the positioning 
of chromosomes, formation of chromatin loops, and interactions between 
regulatory elements such as promoters and enhancers. The dysregulation of 3D 
genome organization has been increasingly recognized as a significant factor in 
cancer development and progression. We aim to understand the molecular 
mechanisms that enable control of 3D genome organization. Understanding these 
control mechanisms will be essential for identifying novel therapeutic 
strategies.

We offer:

  *   Collaborative and supportive research environment
  *   State-of-the-art laboratory facilities
  *   Mentorship from experienced researchers and professors
  *   Access to a vibrant scientific community
  *   Opportunities for national and international collaborations


You will play a pivotal role in conducting experiments, analysing data, and 
interpreting results. You will engage in interdisciplinary research that 
combines structural biology, molecular biology, genomics, and bioinformatics to 
gain a holistic understanding of molecular mechanisms that enable control of 3D 
genome organisation.

1. Postdoc 
level:
 The initial closing date for applications is 8th April 2024, however 
applications will be reviewed and interviewed on an ongoing basis until this 
vacancy is filled.

2. Research Assistant 
level: The 
successful candidate should have a BSc, MSc or PhD Degree in a relevant field. 
The closing date is 18 Apr 2024

3. PhD 
Studentship:
 The closing date is Monday 29th April.


Should you have any questions, please do not hesitate to contact me.

Daniel Panne
Department of Molecular and Cell Biology
University of Leicester
Wellcome Trust Investigator







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[ccp4bb] Positions available UK

[Panne, Daniel (Prof.)]

Dear all,

We currently have Postdoc positions available in our group funded by the 
Wellcome Trust. Our project focuses on understanding molecular mechanisms that 
control the regulation of 3D genome organisation and how they contribute to 
different aspects of genome function. The project is an interdisciplinary, 
collaborative and international project involving groups in Imperial College 
London, the Netherlands Cancer Institute (NKI) Amsterdam, the University of 
Oxford, and the University of Leicester, UK. We combine expertise in structural 
biology, biochemistry, cell biology, model organisms and integrative imaging 
across scales. The aim is to link atomic structures to molecular mechanisms and 
organismal function.

We are seeking creative and highly motivated scientists that are keen to work 
on interdisciplinary projects in an international setting. You should have a 
PhD degree in structural biology or equivalent and have a demonstrated record 
of accomplishment in conducting high quality original research. Experience in 
protein biochemistry and single particle cryoEM or xray crystallography, are 
essential. Depending on interests, fellows can develop additional skills in 
cellular imaging using cryoET.

We offer a well-balanced training programme focused on transferable skills for 
scientists. Workshops cover career development, research integrity/good 
scientific practice and open science and data management initiatives. In 
addition, fellows can complete trainings of their choice based on their future 
career goals and interests.

Applicants are required to outline their suitability for this role via the 
online application process and should include a CV, summary of their 
accomplishment and research interests, and publication list.

The initial closing date for applications is 22th March 2024, however 
applications will be reviewed and interviewed on an ongoing basis until this 
vacancy is filled.

Research Associate; Structural biology of genome 
regulation
For further information about this role please contact Daniel Panne 
(daniel.pa...@le.ac.uk).



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[ccp4bb] PhD student and postdoc positions available

[Panne, Daniel (Prof.)]

We have currently PhD Student and Postdoc positions available at the Leicester 
Institute for Structural and Chemical Biology, UK. Our group focuses on 
understanding how 3D genome organisation contributes to various aspects of 
genome function and how signalling pathways control signal processing on 
enhancers. For examples of recent work see NMSB 30, 853–859 (2023) ; Nature 
Comm 13, 7759 (2022) ; Nature 578, 472–476 (2020); NSMB 27, 233–239 (2020); 
Nature 562, 538–544 (2018).

1. Postdoc positions: Application deadline: 7th January 2024
https://jobs.le.ac.uk/vacancies/9270/research-associate-structural-biology-of-genome-regulation.html

2. 4 year studentship positions funded by BBSRC MIBTP: Application deadline 
4thJanuary 2024
https://le.ac.uk/-/media/uol/docs/study/funded-ops/2024-project/mibtp/panne-daniel-mibtp.docx

We are located at the University of Leicester, home to the Leicester Institute 
for Structural and Chemical Biology (LISCB; https://le.ac.uk/liscb) a centre of 
research excellence. Research within LISCB targets the functioning of 
biological relevant molecules through integrated structural biology approaches 
including CryoEM, chemistry and functional studies.

We have excellent access to state-of-the-art structural biology technologies 
including a Krios cryo-EM microscope equipped with Falcon 3EC and GATAN K3 
detector as well as the Diamond and ESRF Synchrotrons.

If you have questions concerning these roles, please contact me directly.


All the best,
Daniel
daniel.pa...@le.ac.uk



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[ccp4bb] Job advert: Postdoc position CryoEM

[Panne, Daniel (Prof.)]

Dear all,

We have another open position in our Institute!

The Panne group focuses on signal processing on enhancers and how 3D genome 
organisation contributes to various aspects of genome function. For examples of 
recent work see Nature 578, 472–476 (2020); NSMB 27, 233–239 (2020); Nature 
562, 538–544 (2018).

We are located at the the Leicester Institute of Structural and Chemical 
Biology (LISCB), a cross-disciplinary entity that brings together 
internationally renowned research in structural biology, single molecule 
approaches and chemical biology at the University of Leicester. The Institute 
provides access to world-class research facilities, including X-ray 
crystallography, biological NMR spectroscopy, single molecule microscopy and 
the state-of-the-art Midlands Regional Cryo-EM facility.

About you
Successful candidate should have a background in structural studies by single 
particle cryoEM. They must have a track record in conducting internationally 
competitive research. We are looking for a creative and ambitious person with 
good communication skills and keen to work on challenging projects.

LISCB is a flagship research institute recently established by the University 
of Leicester, UK. Our state-of-the-art cryoEM facility houses a TFS Titan Krios 
G3 equipped with a Bioquantum-K3, screening microscope and ancillary equipment. 
For further information and to apply please see the link below:

Research Associate (Structural Biology of Genome 
Regulation)

Closing date is 11 December 2022.

Please get in touch if there are questions concerning this role!

All the best,

--
Daniel Panne
Professor of Structural Biology
Department of Molecular and Cell Biology
University of Leicester
Lancaster Road, Leicester, LE1 7RH, UK
T: +44 (0) 116 229 7408
daniel.pa...@le.ac.uk



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[ccp4bb] reminder Postdoc CryoEM postion -deadline August 31

[Panne, Daniel (Prof.)]

Dear all,

A reminder that we currently have an open postdoc position in our Institute! 
Closing date is August 31st 2022.
 
The Panne group focuses on signal processing on enhancers and how 3D genome 
organisation contributes to various aspects of genome function. For examples of 
recent work see Nature 578, 472–476 (2020); NSMB 27, 233–239 (2020); Nature 
562, 538–544 (2018).

We are located at the the Leicester Institute of Structural and Chemical 
Biology (LISCB) is a cross-disciplinary entity that brings together 
internationally renowned research in structural biology, single molecule 
approaches and chemical biology at the University of Leicester. The Institute 
provides access to world-class research facilities, including X-ray 
crystallography, biological NMR spectroscopy, single molecule microscopy and 
the state-of-the-art Midlands Regional Cryo-EM facility.

About you
Successful candidate should have a background in structural studies by single 
particle cryoEM. They must have a track record in conducting internationally 
competitive research. We are looking for a creative and ambitious person with 
good communication skills and keen to work on challenging projects.

LISCB is one of five flagship research institutes recently established by the 
University of Leicester, UK. We have excellent access to state-of-the-art 
structural biology technologies including a Krios cryo-EM microscope equipped 
with K3/BioQuantum and in house GPU cluster for data processing.

For further information and to apply please see the link below:

https://jobs.le.ac.uk/vacancies/4527/research-associate-structural-biology-of-genome-regulation.html

Please get in touch if you have questions concerning this role.

All the best,

Daniel Panne
Department of Molecular and Cell Biology
University of Leicester
Lancaster Road, Leicester, LE1 7RH, UK
T: +44 (0) 116 229 7408



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[ccp4bb] Job advert: Postdoc CryoEM

[Panne, Daniel (Prof.)]

Dear all,

We currently have an open postdoc position in our Institute!

The Panne group focuses on signal processing on enhancers and how 3D genome 
organisation contributes to various aspects of genome function. For examples of 
recent work see Nature 578, 472–476 (2020); NSMB 27, 233–239 (2020); Nature 
562, 538–544 (2018).

We are located at the the Leicester Institute of Structural and Chemical 
Biology (LISCB) is a cross-disciplinary entity that brings together 
internationally renowned research in structural biology, single molecule 
approaches and chemical biology at the University of Leicester. The Institute 
provides access to world-class research facilities, including X-ray 
crystallography, biological NMR spectroscopy, single molecule microscopy and 
the state-of-the-art Midlands Regional Cryo-EM facility.

About you
Successful candidate should have a background in structural studies by single 
particle cryoEM. They must have a track record in conducting internationally 
competitive research. We are looking for a creative and ambitious person with 
good communication skills and keen to work on challenging projects.

LISCB is one of five flagship research institutes recently established by the 
University of Leicester, UK. We have excellent access to state-of-the-art 
structural biology technologies including a Krios cryo-EM microscope equipped 
with K3/BioQuantum and in house GPU cluster for data processing.

For further information and to apply please see the link below:

Research Associate (Structural Biology of Genome 
Regulation)

Closing date is August 31st 2022.

All the best,

--
Daniel Panne
Professor of Structural Biology
Department of Molecular and Cell Biology
University of Leicester
Lancaster Road, Leicester, LE1 7RH, UK
T: +44 (0) 116 229 7408
daniel.pa...@le.ac.uk




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[ccp4bb] Full-time, Permanent Lecturer and Postdoc positions UK

[Panne, Daniel (Prof.)]

Dear all,
We have currently an opening for a Full-time, Permanent Lecturer position and 
two Postdoc positions available at the Department of Molecular and Cell Biology 
& Leicester Institute for Structural and Chemical Biology, UK.

Postdoc positions: Application deadline: 11 April 2022
1. Research Associate (Structural Biology of Genome 
Regulation)
2. Research Associate (Structural Biology of Genome 
Regulation)

These positions are in the Panne group: The lab focuses on structural biology 
in the area of chromosome biology & gene regulation and infection & immunity 
research. For examples of recent work see Nature 578, 472–476 (2020); NSMB 27, 
233–239 (2020); Nature 562, 538–544 (2018).

Full-time, Permanent Lecturer position: Application deadline: 25 April 2022
1. https://jobs.le.ac.uk/vacancies/5035/lecturer.html
This is a broad call! We are looking for candidates that will address an 
important biological problem using approaches which are complementary or 
synergistic with existing research interests. Any structural biology, single 
molecule & computational biology would be suitable.

If you have questions concerning these roles, please get in touch.

Daniel Panne




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[ccp4bb] multiple Student and Postdoc positions UK

[Panne, Daniel (Prof.)]

Dear all,
We have currently multiple Student and Postdoc positions available at the 
Leicester Institute for Structural and Chemical Biology, UK. Our lab focuses on 
structural biology in the area of chromosome biology & gene regulation and 
infection & immunity research. For examples of recent work see Nature 578, 
472–476 (2020); NSMB 27, 233–239 (2020); Nature 562, 538–544 (2018).

Postdoc positions: Application deadline: 11 April 2022

1. Research Associate (Structural Biology of Genome 
Regulation)

2. Research Associate (Structural Biology of Genome 
Regulation)

Student positions: Application deadline: 11 March 2022

1. 
https://le.ac.uk/study/research-degrees/funded-opportunities/future-100-phd-cls

2. https://le.ac.uk/study/research-degrees/funded-opportunities/liscb


If you have questions concerning these roles, please contact me directly.

All the best,
Daniel Panne
--
Daniel Panne
Department of Molecular and Cell Biology
University of Leicester
Lancaster Road, Leicester, LE1 7RH, UK
T: +44 (0) 116 229 7408




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[ccp4bb] Several PhD & Postdoc positions Leicester, UK

[Panne, Daniel (Prof.)]

This is a reminder that we have several open positions currently available:

We are looking for PhD & postdoctoral researchers to join our lab our lab at 
the Leicester Institute for Structural and Chemical Biology, UK. The positions 
are funded by a 5 year Wellcome Trust Investigator award to work on the 
regulation of gene expression and 3D genome organisation. For examples of 
recent work see Nature 578, 472–476 (2020); NSMB 27, 233–239 (2020); Nature 
562, 538–544 (2018)

The successful candidates will use a multi-disciplinary approach that includes 
preparative biochemistry of multi-protein complexes, protein engineering and 
biophysical and structural techniques. The group is part of the Leicester 
Institute of Structural and Chemical Biology, UK. We work in a highly collegial 
environment and have excellent access to state-of-the-art structural biology 
technologies including a Krios cryo-EM microscope.

Please apply at: 
https://jobs.le.ac.uk/vacancies/2872/research-associate-structural-biology-of-genome-regulation.html

The advert closes on November 28!

For PhD level positions please apply at: 
https://more.bham.ac.uk/mrc-aim/phd-opportunities/

The advert closes on January 09!

If you have questions, please contact me directly.
All the best,

Daniel Panne
Professor of Structural Biology
Department of Molecular and Cell Biology
University of Leicester
Email: daniel.pa...@le.ac.uk




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[ccp4bb] Postdoc positions Leicester, UK

[Panne, Daniel (Prof.)]

Dear all,

We are looking for postdoctoral researchers to join our lab our lab at the 
Leicester Institute for Structural and Chemical Biology, UK. The positions are 
funded by a 5 year Wellcome Trust Investigator award to work on the regulation 
of gene expression and 3D genome organisation. For examples of recent work see 
Nature 578, 472–476 (2020); NSMB 27, 233–239 (2020); Nature 562, 538–544 (2018)

The successful candidates will use a multi-disciplinary approach that includes 
preparative biochemistry of multi-protein complexes, protein engineering and 
biophysical and structural techniques. The group is part of the Leicester 
Institute of Structural and Chemical Biology, UK. We have excellent access to 
state-of-the-art structural biology technologies including a Krios cryo-EM 
microscope

Please apply at: 
https://jobs.le.ac.uk/vacancies/2872/research-associate-structural-biology-of-genome-regulation.html

The advert closes on November 28!

If you have questions concerning this role, please contact me directly.
All the best,
Daniel

--

Daniel Panne
Professor of Structural Biology
Department of Molecular and Cell Biology
University of Leicester
Email: daniel.pa...@le.ac.uk



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[ccp4bb] Reminder – Postdoc positions Leicester, UK

[Panne, Daniel (Prof.)]

The advert closes on August 31st.

We are looking for postdoctoral researchers to join our lab our lab at the 
Leicester Institute for Structural and Chemical Biology, UK. The positions are 
funded by a 5 year Wellcome Trust Investigator award to work on the regulation 
of gene expression and 3D genome organisation. For examples of recent work see 
Nature 578, 472–476 (2020); NSMB 27, 233–239 (2020); Nature 562, 538–544 (2018)

The successful candidates will use a multi-disciplinary approach that includes 
preparative biochemistry of multi-protein complexes, protein engineering and 
state-of-the-art biophysical and structural techniques. The group is part of 
the Leicester Institute of Structural and Chemical Biology, UK. We have 
excellent access to state-of-the-art structural biology technologies including 
a Krios cryo-EM microscope

Please apply at: 
https://jobs.le.ac.uk/vacancies/2872/research-associate-structural-biology-of-genome-regulation.html

If you have questions concerning this role, please contact me directly.
All the best,
Daniel

--

Daniel Panne
Professor of Structural Biology
Department of Molecular and Cell Biology
University of Leicester
Email: daniel.pa...@le.ac.uk



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[ccp4bb] Postdoc positions Leicester, UK

[Panne, Daniel (Prof.)]

Dear all,

We are looking for postdoctoral researchers to join our lab our lab at the 
Leicester Institute for Structural and Chemical Biology, UK. The positions are 
funded by a 5 year Wellcome Trust Investigator award to work on the regulation 
of gene expression and 3D genome organisation. For examples of recent work see 
Nature 578, 472–476 (2020); NSMB 27, 233–239 (2020); Nature 562, 538–544 (2018)

The successful candidates will use a multi-disciplinary approach that includes 
preparative biochemistry of multi-protein complexes, protein engineering and 
state-of-the-art biophysical and structural techniques. The group is part of 
the Leicester Institute of Structural and Chemical Biology, UK. We have 
excellent access to state-of-the-art structural biology technologies including 
a Krios cryo-EM microscope

The advert closes on August 31st.

Please apply at: 
https://jobs.le.ac.uk/vacancies/2872/research-associate-structural-biology-of-genome-regulation.html

If you have questions concerning this role, please contact me directly.
All the best,
Daniel

--

Daniel Panne
Professor of Structural Biology
Department of Molecular and Cell Biology
University of Leicester
Email: daniel.pa...@le.ac.uk



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[ccp4bb] Postdoc position UK – deadline 13 May 2021

[Panne, Daniel (Prof.)]

Dear all,

We have an open postdoc position available in our lab at the Leicester 
Institute for Structural and Chemical Biology, UK. Our group focuses on signal 
processing on enhancers and how 3D genome organisation contributes to various 
aspects of genome function. For examples of recent work see Nature 578, 472–476 
(2020); NSMB 27, 233–239 (2020); Nature 562, 538–544 (2018).

The successful candidates will use a multi-disciplinary approach that includes 
preparative biochemistry of multi-protein complexes, protein engineering and 
state-of-the-art biophysical and structural techniques.

The advert closes on 13 May 2021!

Please apply at: 
https://jobs.le.ac.uk/vacancies/2872/research-associate-structural-biology-of-genome-regulation.html

If you have questions concerning this role, please contact me directly.

All the best,
Daniel

--
Daniel Panne
Professor of Structural Biology
Department of Molecular and Cell Biology
University of Leicester
Lancaster Road, Leicester, LE1 7RH, UK
T: +44 (0) 116 229 7408
daniel.pa...@le.ac.uk



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[ccp4bb] PhD positions UK

[Panne, Daniel (Prof.)]

Dear all,

Could you please forward the following opportunities to suitable candidates?

We ave two fully funded PhD studentship positions available in our laboratory. 
Our group studies higher–order signalling complexes that are important in 
gene/chromatin regulation and assembly (e.g. see Nature 578, 472–476 (2020); 
NSMB 27, 233–239 (2020); Nature 562, 538–544 (2018). The group is part of a new 
Institute for Structural and Chemical Biology at the University of Leicester 
which has excellent access to state-of-the-art structural biology technologies.

Further particulars, including details on how to apply can be accessed online.

Position 1 (deadline 04 May): 
https://www.findaphd.com/phds/project/structural-biology-of-genome-folding/?p131682
Position 2 (deadline 06 May): 
https://www.findaphd.com/phds/project/structural-mechanism-of-signal-dependent-gene-transcription/?p126965


Thanks and all the best,
Daniel





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[ccp4bb] Postdoc position UK – deadline April 12

[Panne, Daniel (Prof.)]

Dear all,

We have an open postdoc position available in our lab at the Leicester 
Institute for Structural and Chemical Biology, UK. Our group focuses on signal 
processing on enhancers and how 3D genome organisation contributes to various 
aspects of genome function. For examples of recent work see Nature 578, 472–476 
(2020); NSMB 27, 233–239 (2020); Nature 562, 538–544 (2018).

The successful candidates will use a multi-disciplinary approach that includes 
preparative biochemistry of multi-protein complexes, protein engineering and 
state-of-the-art biophysical and structural techniques.

The advert closes on April 12!

Please apply at: 
https://jobs.le.ac.uk/vacancies/2872/research-associate-structural-biology-of-genome-regulation.html

If you have questions concerning this role, please contact me directly.

All the best,
Daniel

--
Daniel Panne
Professor of Structural Biology
Department of Molecular and Cell Biology
University of Leicester
Lancaster Road, Leicester, LE1 7RH, UK
T: +44 (0) 116 229 7408
daniel.pa...@le.ac.uk



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[ccp4bb] PostDoc position in UK

[Panne, Daniel (Prof.)]

Dear all,

We have an open postdoc position available in our lab at the Leicester 
Institute for Structural and Chemical Biology, UK. Our group focuses on signal 
processing on enhancers and how 3D genome organisation contributes to various 
aspects of genome function. For examples of recent work see Nature 578, 472–476 
(2020); NSMB 27, 233–239 (2020); Nature 562, 538–544 (2018).

The successful candidates will use a multi-disciplinary approach that includes 
preparative biochemistry of multi-protein complexes, protein engineering and 
state-of-the-art biophysical and structural techniques.
The advert closes on April 12!

Please apply at: 
https://jobs.le.ac.uk/vacancies/2872/research-associate-structural-biology-of-genome-regulation.html

If you have questions concerning this role, please contact me directly.

All the best,
Daniel

--
Daniel Panne
Professor of Structural Biology
Department of Molecular and Cell Biology
University of Leicester
Lancaster Road, Leicester, LE1 7RH, UK
T: +44 (0) 116 229 7408
daniel.pa...@le.ac.uk




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Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

[Panne, Daniel (Prof.)]

I agree with Phil!

Yes, it is nice to be able to obtain better models but interesting biological 
function resides usually in the most variable and least predictable features of 
a protein, how it associates with other proteins etc. Even when a fold can 
predicted, such folds alone frequently fail to predict function (which doomed 
structural genomics from the outset).

Daniel




On 11 Dec 2020, at 12:42, Phil Evans 
mailto:p...@mrc-lmb.cam.ac.uk>> wrote:

Alpha-fold looks great and is clearly a long way towards answering the question 
“this is the sequence, what is the structure?”

But I’ve always thought the more interesting question is “this is the 
structure, what does it do?”  Is there any progress on that question?

Phil


On 11 Dec 2020, at 12:12, Tristan Croll 
mailto:ti...@cam.ac.uk>> wrote:

I'm not Randy, but I do have an answer: like this. This is T1049-D1. AlphaFold 
prediction in red, experimental structure (6y4f) in green. Agreement is close 
to perfect, apart from the C-terminal tail which is way off - but clearly 
flexible and only resolved in this conformation in the crystal due to packing 
interactions. GDT_TS is 93.1; RMS_CA is 3.68 - but if you exclude those tail 
residues, it's 0.79. With an alignment cutoff of 1 A, you can align 109 of 134 
CAs with an RMSD of 0.46 A.
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Leonid Sazanov mailto:saza...@ist.ac.at>>
Sent: 11 December 2020 10:36
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less 
pipetting (?)

Dear Randy,

Can you comment on why for some of AplhaFold2 models with GDT_TS > 90 
(supposedly as good as experimental model) the RMS_CA (backbone) is > 3.0 
Angstrom? Such a deviation can hardly be described as good as experimental. 
Could it be that GDT_TS is kind of designed to evaluate how well the general 
sub-domain level fold is predicted, rather than overall detail?

Thanks,
Leonid



Several people have mentioned lack of peer review as a reason to doubt the 
significance of the AlphaFold2 results.  There are different routes to peer 
review and, while the results have not been published in a peer review journal, 
I would have to say (as someone who has been an assessor for two CASPs, as well 
as having editorial responsibilities for a peer-reviewed journal), the peer 
review at CASP is much more rigorous than the peer review that most papers 
undergo. The targets are selected from structures that have recently been 
solved but not published or disseminated, and even just tweeting a C-alpha 
trace is probably enough to get a target cancelled.  In some cases (as we’ve 
heard here) the people determining the structure are overly optimistic about 
when their structure solution will be finished, so even they may not know the 
structure at the time it is predicted.  The assessors are blinded to the 
identities of the predictors, and they carry out months of calculations and 
inspections of the models, computing ranking scores before they find out who 
made the predictions.  Most assessors try to bring something new to the 
assessment, because the criteria should get more stringent as the predictions 
get better, and they have new ideas of what to look for, but there’s always 
some overlap with “traditional” measures such as GDT-TS, GDT-HA (more stringent 
high-accuracy version of GDT) and lDDT.



Of course we’d all like to know the details of how AlphaFold2 works, and the 
DeepMind people could have been (and should be) much more forthcoming, but 
their results are real.  They didn’t have any way of cheating, being selective 
about what they reported, or gaming the system in any other way that the other 
groups couldn’t do.  (And yes, when we learned that DeepMind was behind the 
exceptionally good results two years ago at CASP13, we made the same half-jokes 
about whether Gmail had been in the database they were mining!)



Best wishes,



Randy Read



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Re: [ccp4bb] Advice on DNA negative staining

[Panne, Daniel (Prof.)]

Hi Meytal,

1. The concentration seems way too high at 254mg/ml. Typically 0.1-5mg/ml are 
used.
2. Uranyl ions react with phosphate groups resulting in positive stain. The 
resulting contrast is frequently poor.
3. Rotary shadowing can be used to enhance contrast.

Best,
Daniel


On 4 Aug 2020, at 11:20, Marin van Heel 
<057a89ab08a1-dmarc-requ...@jiscmail.ac.uk>
 wrote:


Dear Meytal,

Suggestion: Apply a strong high-pass filter to the images before visually 
judging them!

Marin

On Tue, Aug 4, 2020 at 3:50 AM Meytal Galilee 
mailto:meytal.gali...@gmail.com>> wrote:
Hi Arunabh Athreya,
Sure (this is the linear 2200 b.p. at 175uM)




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From: Arunabh Athreya mailto:arun...@iisc.ac.in>>
Sent: Tuesday, August 4, 2020, 12:54
To: CCP4BB@JISCMAIL.AC.UK; Meytal Galilee
Subject: Re: Advice on DNA negative staining

Hi Meytal

Do you have an EM image snapped from your negative staining sample?

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[ccp4bb] PhD studentships at University of Leicester, UK

[Panne, Daniel (Prof.)]

Dear all,
Could you please forward the following opportunities to suitable candidates?

Applications are invited for BBSRC funded PhD studentships positions in the 
laboratory of Prof Daniel Panne. The group studies higher–order signalling 
complexes that are important in gene/chromatin regulation and assembly (e.g. 
see Nature 2018, 562(7728):538-544). The group is part of a new Institute for 
Structural and Chemical Biology at the University of Leicester which has 
excellent access to state-of-the-art structural biology technologies.

Further particulars, including details on how to apply can be accessed online.

Deadline 6 January: 
http://www.findaphd.com?pj=116664
Deadline 12 January: 
https://warwick.ac.uk/fac/cross_fac/mibtp/pgstudy/phd_opportunities/structural_biology/gene_transcription


Thanks and all the best,
Daniel








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[ccp4bb] Postdoctoral position in structural biology at Leicester, UK

[Panne, Daniel (Prof.)]

We are looking to recruit highly motivated and ambitious individual to take a 
leading role in investigating higher–order signaling complexes in gene and 
chromatin regulation.
The Panne group uses X-ray crystallography and cryo electron microscopy to 
study higher–order signaling complexes that are important in 
inflammatory/cancer signaling and gene/chromatin regulation and assembly (e.g. 
see Nature 2018, 562(7728):538-544).
The successful candidate should have a strong background and interest in 
biochemistry and structural biology. We are looking for a creative and 
ambitious person with good communication skills and keen to work on a 
challenging project.
Experience in biochemistry of protein complexes, insect cell expression 
systems, X-ray crystallography or cryo-electron microscopy would be 
particularly beneficial. The group is part of the Leicester Institute of 
Structural and Chemical Biology (LISCB one of five flagship research institutes 
recently established by the University of Leicester, UK. We have excellent 
access to state-of-the-art structural biology technologies including a Krios 
cryo-EM microscope equipped with Falcon 3EC and GATAN K2 (planned upgrade to K3 
in early 2019) detector as well as the Diamond and ESRF Synchrotrons.
You can find out more about this vacancy by contacting 
daniel.pa...@le.ac.uk
Please apply online at 
https://jobs.le.ac.uk/vacancies/vacancy-details.aspx?VacancyID=162=1



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[ccp4bb] Postdoctoral Research fellow position - closing date 22 Nov 2018

[Panne, Daniel (Prof.)]

The Leicester Institute of Structural and Chemical Biology (LISCB) is one of 
five flagship research institutes recently established by the University of 
Leicester, UK. LISCB brings together internationally renowned research using 
structural biology, chemical biology and single molecule methods to investigate 
major challenges in fundamental biological processes. We are seeking to recruit 
a postdoctoral researcher to join the group of Prof Daniel Panne. The focus is 
on multi-protein complexes that are relevant in cancer biology and human 
disease including epigenetic gene/chromatin regulation and signaling in the 
innate immune system. The primary experimental techniques include protein 
crystallography, electron microscopy, protein expression, biochemistry.

For examples of recently published work please see e.g. Nature DOI: 
10.1038/s41586-018-0621-1.

Please go to 
https://jobs.le.ac.uk/vacancies/vacancy-details.aspx?VacancyID=162=1 
for more information and to apply.

For informal queries please contact me directly.

best,
Daniel

--
Daniel Panne
Professor of Structural Biology
Department of Molecular and Cell Biology
University of Leicester
Lancaster Road, Leicester, LE1 7RH, UK
T: +44 (0) 116 229 7408
daniel.pa...@le.ac.uk




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