CCP4 - Collaborative Computing Project in structural biology

Lead Research Organisation: BBSRC

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Technical Summary

The overarching aim of the proposal is to transform the ability of biologists to pursue International level structural research. We have chosen this theme because we recognise that structural biology is evolving to tackle increasingly complex and exciting biological projects. This emphasis on biology has inevitably decreased the amount of training in X-ray|crystallography. The gap in expertise is the most serious for the most difficult projects. Achieving our aim will enable biologists to undertake more challenging problems, to get the best from their data, to accelerate the computational process and to produce more reliable insights. |The project has four objectives.|1. Development of new methods for reliably and automatically building accurate atomic models for structures at limited resolution (Post 1).|2. Development of software to handle the next generation of X-ray detectors and to extract diffraction data from images from poor crystals (Post 2).|3. Development of new expert wizard based software and databases to guide the inexperienced user to get the most from the data by presenting not only information but strategy for progress, whilst still allowing the experienced user the flexibility that is the hallmark of CCP4 (Post 3).|4. Translation of the software developments of the first three objectives, and those of other CCP4 staff and contributors, into robust, well supported, and widely used tools for Industry and Academia (Post 4). This will demonstrate successful technology transfer.

Publications

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Evans PR (2011) An introduction to data reduction: space-group determination, scaling and intensity statistics. in Acta crystallographica. Section D, Biological crystallography

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Parkhurst JM (2014) : the diffraction experiment toolbox. in Journal of applied crystallography

 
Description Training of scientists
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
 
Description Workshops, tutorials and lectures on data processing
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
 
Title Crystallographic software 
Description The program MOSFLM is used to process data from multiple detectors. 
Type Of Material Improvements to research infrastructure 
Year Produced 2006 
Provided To Others? Yes  
Impact The Nobel prize won by Ramakrishnan depended in part on CCP4 software 
 
Description Diamond 
Organisation Diamond Light Source
Country United Kingdom 
Sector Academic/University 
PI Contribution Set up automated data processing
Impact Many data sets processed at Diamond
Start Year 2009
 
Description ESRF 
Organisation European Synchrotron Radiation Facility
Department X-ray Group
Country France 
Sector Academic/University 
PI Contribution Data processing (EDNA)
Impact Many data sets processed
Start Year 2006
 
Title Code 
Description Code developed to process data from new detectors 
IP Reference  
Protection Copyrighted (e.g. software)
Year Protection Granted 2007
Licensed Yes
Impact Processing data sets
 
Description Schools visits 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Each year I host visits to my lab from local secondary school (10's of pupils) and I also give a talk to visiting school pupils on science (approx 50 pupils).

Some of the children seemed to appreciate that chemistry was important in biology.
Year(s) Of Engagement Activity Pre-2006,2006,2007,2008,
 
Description Training and workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Between 20 to 50 pupils per year visit St Andrews and as part of this, they are exposed to structural biology.

Teachers report increased enthusiasm for biomedical science
Year(s) Of Engagement Activity 2006,2007,2008,2009,2010
 
Description workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Helped in the training of post-graduate students in structural biology at the following meetings.
CCP4/ZCAM workshop, Zaragoza, Spain March 2012
CCP4/ APS workshop, Argonne, USA, June 2012
CCP4/APS workshop, Argonne, USA, June 2013
CCP4/CeBEM workshop, Montevideo, Uruguay, April 2013

Widespread use of UK authored software.
Year(s) Of Engagement Activity 2013,2014
URL http://www.ccp4.ac.uk