Re: [ccp4bb] protein protein interactions

[00000c2488af9525-dmarc-request]

Hello, if you mean theoretical docking, here is an old list of links:https://zlab.umassmed.edu/zdock/dockingsites.shtmlSome of these will still be maintained.Jon CooperOn 10 Feb 2020 16:50, Sarah Bowman  wrote:

Hi Careina,
 
There’s a program called FRODOCK that generates predictions of how two proteins could interact:
http://chaconlab.org/modeling/frodock
 
Cheers,
Sarah
 

Sarah EJ Bowman, PhD
 
Associate Research Scientist, Hauptman-Woodward Medical Research Institute
Director, High-Throughput Crystallization Screening Center
 
Research Webpage
www.getacrystal.org


 
 

From: CCP4 bulletin board  on behalf of "careinaedgooms@yahoo.com" <02531c126adf-dmarc-request@JISCMAIL.AC.UK>
Reply-To: "careinaedgooms@yahoo.com" 
Date: Monday, February 10, 2020 at 11:17 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Fw: protein protein interactions


 



 










 









Dear all


Apologies for off topic question but can anyone recommend good programs for identifying docking interfaces between two proteins. I do not know that these two proteins
 interact. I would like a level of confidence on a possible interaction. is there a good program to do this?


kind regards


Careina













 



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[ccp4bb] Postdoctoral positions(2) in cryo-EM

[Alessandro Vannini]

Dear all,
I would like to draw your attention to two postdoctoral positions available 
immediately in my laboratory to work on cryo-EM determination of complexes 
operating at the interface of SMC complexes and the transcription apparatus. 
The projects are well suited for individual with good experience in modern 
Cryo-EM pipelines. For some projects datasets have been already collected and 
await further processing while others samples are “cryo” ready. The 
postdoctoral fellows will be based at the ICR in South Kensington (Glacios, F20 
in house + consortium Krios + eBIC) but is expected that will also benefit from 
the top notch EM facility currently being set up at the Human Technopole, Milan 
Italy (Krios, Glacios, Talos, Aquilos, CLEM and room temperature tomography 300 
Kv scope).
If interested please apply here:

https://icr.tal.net/vx/appcentre-ext/brand-0/candidate/so/pm/1/pl/1/opp/995-Postdoctoral-Training-Fellow-in-Cryo-EM/en-G

For general enquiries please write me directly.

Cheers,

Alessandro 


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[ccp4bb] Fwd: [ccp4bb] Fw: protein protein interactions

[RUBEN SANCHEZ GARCIA]

Dear Careina,

I would recommend you our partner-specific binding site predictor:  
BIPSPI, that uses as input 2 sequences or 2 pdb files and proposes the  
binding site of the two partners.


http://bipspi.cnb.csic.es/xgbPredApp/

Kind regards,

Ruben


Quoting "careinaedgo...@yahoo.com"  
<02531c126adf-dmarc-requ...@jiscmail.ac.uk>:


Dear allApologies for off topic question but can anyone recommend  
good programs for identifying docking interfaces between two  
proteins. I do not know that these two proteins interact. I would  
like a level of confidence on a possible interaction. is there a  
good program to do this?kind regardsCareina




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- End forwarded message -




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--- Begin Message ---

Dear Careina,

I would recommend you our partner-specific binding site predictor:  
BIPSPI, that uses as input 2 sequences or 2 pdb files and proposes the  
binding site of the two partners.


http://bipspi.cnb.csic.es/xgbPredApp/

Kind regards,

Ruben


Quoting "careinaedgo...@yahoo.com"  
<02531c126adf-dmarc-requ...@jiscmail.ac.uk>:


Dear allApologies for off topic question but can anyone recommend  
good programs for identifying docking interfaces between two  
proteins. I do not know that these two proteins interact. I would  
like a level of confidence on a possible interaction. is there a  
good program to do this?kind regardsCareina




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--- End Message ---

Re: [ccp4bb] protein protein interactions

[Sarah Bowman]

Hi Careina,

There’s a program called FRODOCK that generates predictions of how two proteins 
could interact:
http://chaconlab.org/modeling/frodock

Cheers,
Sarah

Sarah EJ Bowman, PhD

Associate Research Scientist, Hauptman-Woodward Medical Research Institute
Director, High-Throughput Crystallization Screening Center

Research Webpage
www.getacrystal.org


From: CCP4 bulletin board  on behalf of 
"careinaedgo...@yahoo.com" <02531c126adf-dmarc-requ...@jiscmail.ac.uk>
Reply-To: "careinaedgo...@yahoo.com" 
Date: Monday, February 10, 2020 at 11:17 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Fw: protein protein interactions



Dear all
Apologies for off topic question but can anyone recommend good programs for 
identifying docking interfaces between two proteins. I do not know that these 
two proteins interact. I would like a level of confidence on a possible 
interaction. is there a good program to do this?
kind regards
Careina



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Re: [ccp4bb] Fw: protein protein interactions

[Eleanor Dodson]

pisa is good at this.
Are they in the same pdb file?
Eleanor

On Mon, 10 Feb 2020 at 16:16, careinaedgo...@yahoo.com <
02531c126adf-dmarc-requ...@jiscmail.ac.uk> wrote:

>
>
> Dear all
> Apologies for off topic question but can anyone recommend good programs
> for identifying docking interfaces between two proteins. I do not know that
> these two proteins interact. I would like a level of confidence on a
> possible interaction. is there a good program to do this?
> kind regards
> Careina
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Fw: protein protein interactions

[careinaedgo...@yahoo.com]

 
  
 Dear allApologies for off topic question but can anyone recommend good 
programs for identifying docking interfaces between two proteins. I do not know 
that these two proteins interact. I would like a level of confidence on a 
possible interaction. is there a good program to do this?kind regardsCareina



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[ccp4bb] Higher Scientific Officer position available at The Institute of Cancer Research, London, UK

[Rob Van Montfort]

The Institute of Cancer Research, London, is one of the world’s most 
influential cancer research institutes, with an outstanding record of 
achievement dating back more than 100 years. We provided the first convincing 
evidence that DNA damage is the basic cause of cancer, laying the foundation 
for the now universally accepted idea that cancer is a genetic disease. Today, 
The Institute of Cancer Research (ICR) leads the world at isolating 
cancer-related genes and discovering new targeted drugs for personalised cancer 
treatment.

The Cancer Research UK Cancer Therapeutics Unit, within the Division of Cancer 
Therapeutics, is a multidisciplinary 'bench to bedside' centre, comprising 
around 160 staff dedicated to the discovery and development of novel 
therapeutics for the treatment of cancer. The Cancer Therapeutics Unit’s 
exciting goal is to discover high quality small molecule drug candidates and to 
progress these to clinical trial. All the scientific disciplines are in place 
to make this possible, including medicinal chemistry, biology, structural 
biology, assay scientists, drug metabolism and clinical specialists who focus 
on new molecular targets emerging from human genome and ground breaking cell 
biology research.

A Higher Scientific Officer position is now available in the Hit Discovery and 
Structural Design Team within the Unit. The team uses biochemical and 
biophysical assays to perform small-molecule high-throughput screening and 
fragment-based hit discovery, coupled with X-ray crystallography to enable 
structure-based drug design within the Unit. These methodologies are 
underpinned by state-of-the art protein expression, purification and 
characterisation capabilities, allowing for the generation of large quantities 
of high quality protein targets. The successful candidate will be involved in 
establishing the expression, purification and characterisation of one of our 
early stage drug targets, using contemporary expression systems and 
purification methods available within the Team. In addition, the post-holder is 
expected to characterise ligand and inhibitor binding to the recombinant 
proteins using biochemical assays and biophysical methods such as Thermal Shift 
Assay (TSA), Surface Plasmon Resonance (SPR), Isothermal Titration Calorimetry 
(ITC) and ligand-based NMR methods. The successful candidate will be an 
integral member of a multidisciplinary project team and will interact closely 
with the biologists, computational chemists, medicinal chemists and structural 
biologists.

Applicants must have a BSc in a biochemistry or related biological subject and 
in depth technical laboratory experience in protein expression and purification 
methodologies. Expertise in insect cell expression, assay development and/or 
knowledge of biophysical methods would be advantageous. The starting salary for 
the positions will be in the range £32,000 to £44,400 p.a. inclusive (based on 
previous experience). The position is currently funded for one year. Informal 
enquiries can be made via email to 
rob.vanmontf...@icr.ac.uk or 
rosemary.bu...@icr.ac.uk. Closing date is 
08/03/2020.

Please DO NOT send your application to Dr van Montfort, or Dr Burke. 
Applications will only be considered if made via the e-recruitment system on 
our website www.icr.ac.uk.


Dr. Rob van Montfort
Reader in Structural Biology and Cancer Drug Discovery
Team Leader Hit Discovery and Structural Design
Divisions of Cancer Therapeutics and Structural Biology
The Institute of Cancer Research
15 Cotswold Road
Sutton SM2 5NG
UK

Tel:
+44-(0)20-8722-4364 (Sutton)
+44-(0)20-7153-5142 (Chelsea)
Email: rob.vanmontf...@icr.ac.uk









The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
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message to the sender by replying to it and then delete the message from your 
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[ccp4bb] Tenure track position in structural bioinformatics (Regensburg, Germany)

[Remco Sprangers]

Dear All,

I would like to draw you attention to an opening for a tenure track 
professor position in "Structural Bioinformatics" at the Regensburg 
university (Germany).


The official add can be found at:

https://www.uni-regensburg.de/universitaet/stellenausschreibungen/professuren/index.html

under the header "W 1 - Juniorprofessur für Strukturelle Bioinformatik 
(mit Tenure Track auf W2)"


With kind regards,

Remco

-
Prof. Dr. Remco Sprangers
Bio-molecular NMR spectroscopy
Institute of  Biophysics and Physical Biochemistry
Faculty of Biology and Preclinical Medicine
University of Regensburg
Universitätsstrasse 31
93053 Regensburg



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