CCP4 - Collaborative Computing Project in structural biology
Lead Research Organisation:
Biotechnology and Biological Sciences Research Council
Department Name: UNLISTED
Abstract
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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.
People |
ORCID iD |
James Naismith (Principal Investigator) |
Publications
Evans PR
(2011)
An introduction to data reduction: space-group determination, scaling and intensity statistics.
in Acta crystallographica. Section D, Biological crystallography
Parkhurst JM
(2014)
dxtbx: 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 | Private |
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-2006,2006,2007,2008,2009,2010,2011,2012,2013,2014 |
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 | 2006,2007,2008,2009,2010,2011,2012,2013 |
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 |