Support for the Protein Circular Dichroism Data Bank and the Dichroweb Analysis Server
Lead Research Organisation:
Queen Mary University of London
Department Name: Sch of Biological and Chemical Sciences
Abstract
Circular Dichroism (CD) spectroscopy is an established and valuable technique for examining protein structure, dynamics, and folding, and is regularly used as a standard method in a large number of UK biological and chemical laboratories. This is a proposal to create a comprehensive electronic archiving and analysis resource for CD spectroscopy that can be used by the structural biology and bioinformatics communities. It will include the running, curation and development of the Protein Circular Dichroism Data Bank (PCDDB), a deposition and searchable data bank for circular dichroism spectra of biomacromolecules. The PCDDB will be a resource for structural molecular biology and bioinformatics, and a public archive for data sharing of spectroscopic data to parallel the Protein Data Bank (PDB), a long-existing and valuable reference data bank for protein crystal and NMR data. This project also includes the operation, upgrading and maintenance of DICHROWEB, a widely-used user-friendly online server for the analysis of circular dichroism data. Together these two bioinformatics facilities will provide a comprehensive package of enabling and supportive resources in CD spectroscopy for the Structural Biology and Bioinformatics communities.
Technical Summary
Circular Dichroism (CD) spectroscopy is an established and valuable technique for examining protein structure, dynamics, and folding, and is regularly used as a fundemental method in a large number of biological and chemical laboratories. This is a proposal to create, curate and maintain a comprehensive electronic archiving and analysis resource for CD spectroscopy that can be used by the academic and industrial structural biology and bioinformatics communities. It will include the running, curation and development of the Protein Circular Dichroism Data Bank (PCDDB), a deposition and searchable data bank for circular dichroism spectra of biomacromolecules. The aim of this data bank is to provide open access and public archiving facilities for circular dichroism spectral data. This project also will include the development of a suite of support tools, such as validation software (which will have benefit for both ensuring the quality of data in the data bank and establishing standards for spectroscopic data used by the academic and industrial structural biology communities, and will be developed as both a deposition-linked online resource and a standalone downloadable version) and spectral matching tools for identification of similar/related spectra and extraction of structural information. This project also includes the upgrading, maintenance and continued operation of DICHROWEB, a widely-used user-friendly online server for the analysis of circular dichroism data. Together these two bioinformatics facilities will provide a comprehensive package of enabling and supportive resources in CD spectroscopy for the structural biology and bioinformatics communities.
People |
ORCID iD |
| Robert Janes (Principal Investigator) |
Publications
Klose DP
(2012)
DichroMatch: a website for similarity searching of circular dichroism spectra.
in Nucleic acids research
Klose DP
(2010)
2Struc: the secondary structure server.
in Bioinformatics (Oxford, England)
Miles AJ
(2008)
Light flux density threshold at which protein denaturation is induced by synchrotron radiation circular dichroism beamlines.
in Journal of synchrotron radiation
Wallace BA
(2010)
Synchrotron radiation circular dichroism (SRCD) spectroscopy: an enhanced method for examining protein conformations and protein interactions.
in Biochemical Society transactions
Whitmore L
(2018)
DichroMatch at the protein circular dichroism data bank (DM@PCDDB): A web-based tool for identifying protein nearest neighbors using circular dichroism spectroscopy.
in Protein science : a publication of the Protein Society
Whitmore L
(2011)
PCDDB: the Protein Circular Dichroism Data Bank, a repository for circular dichroism spectral and metadata.
in Nucleic acids research
Whitmore L
(2010)
The protein circular dichroism data bank, a Web-based site for access to circular dichroism spectroscopic data.
in Structure (London, England : 1993)
Whitmore Lee
(2013)
The Protein Circular Dichroism Data Bank: A Resource for Data Sharing
in BIOPHYSICAL JOURNAL
| Description | This grant enabled development of bioinformatics tools and resources (computer packages and databases) for structural analysis to support the scientific research community |
| Exploitation Route | The technique of circular dichroism could be used in the development of improved pharmaceuticals with increased and more directed interactions with key selected proteins which have a significant reduction in any possible side effects. Our tools can greatly assist in the analysis of the data obtained thereby improving the interpretation of the results from such research. |
| Sectors | Agriculture, Food and Drink,Education,Pharmaceuticals and Medical Biotechnology |
| Description | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Amount | £450,573 (GBP) |
| Funding ID | BB/J019194/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2013 |
| End | 06/2018 |
| Description | Biotechnology and Biological Sciences Research Council (BBSRC) Tools and Resources |
| Amount | £118,022 (GBP) |
| Funding ID | BB/I023887/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2011 |
| End | 04/2013 |
| Description | Collaborative Sino-UK SRCD Spectroscopy Studies |
| Amount | £24,800 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2004 |
| End | 03/2012 |
| Description | FP7 Infrastructure Programme CALIPSO |
| Amount | £10,000 (GBP) |
| Funding ID | 312284 |
| Organisation | European Commission |
| Department | Seventh Framework Programme (FP7) |
| Sector | Public |
| Country | European Union (EU) |
| Start | 06/2012 |
| End | 05/2015 |
| Description | IUPAC |
| Amount | $9,600 (USD) |
| Funding ID | 2010-033-2-024 |
| Organisation | International Union of Pure and Applied Chemistry (IUPAC) |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 06/2010 |
| End | 05/2014 |
| Title | 2Struc |
| Description | Examination of a query entry, being a protein atomic structure, and presenting from it the results from eight different packages describing different ways of evaluating the secondary structure contents. A second component is a comparison package between two (more in NMR models) protein structures identifying the similarities and differences between features in these structures. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2012 |
| Provided To Others? | Yes |
| Impact | The tool is being cited as being used regularly |
| URL | http://2struc.cryst.bbk.ac.uk/ |
| Title | Dichromatch |
| Description | Presents four different ways of evaluating the closest matching (three in each case) Circular Dichroism spectra in a given Reference set of spectra (default are those in the Protein Circular Dichroism Data Bank). |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2012 |
| Provided To Others? | Yes |
| Impact | At this time I am not aware of "notable impacts" that have arisen specifically from this tool however it is well used by researchers. |
| URL | http://dichromatch.cryst.bbk.ac.uk/ |
| Title | PCDDB |
| Description | The Protein Circular Dichroism Data Bank (PCDDB) - offering a repository for CD and Synchrotron Radiation Circular Dichroism (SRCD) spectra and meta data (including experimental/sample data and machine parameters) providing a resource for the science community. This is an ongoing resource being continuously enhanced and enriched by us to provide a secure site for the deposition of CD(SRCD) spectral data and associated meta-data for archiving purposes. This also enables the scientific community to access this data in support of their own research. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2010 |
| Provided To Others? | Yes |
| Impact | Currently well over 500,000 entry downloads by the science community and gaining swiftly in citations |
| URL | http://pcddb.cryst.bbk.ac.uk/home.php |
| Description | Bonnie A Wallace |
| Organisation | Birkbeck, University of London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This is a linked grant where both parties collaborate mutually on many aspects of the work. Our primary directive is creating tools for the resource of various kinds. We jointly contribute in all aspects of the grant. |
| Collaborator Contribution | This is a linked grant where both parties collaborate on many aspects of the work. My collaborator's group is primarily responsible for the maintainance and expansion of the resource and supporting processing website facilities. We jointly contribute in all aspects of the grant. |
| Impact | All of these are multi-disciplinary by the nature of the technique of CD which lends itself to utilisation in many disparate fields of study, and to bioinformatics where the tools can be used as a basis for analysing the content for many reasons (which we are doing ourselves as well) The Protein Circular Dichroism Data Bank website Dichromatch server ValiDichro server Publications Tools to support the resource |
| Description | Robin Maytum |
| Organisation | University of Bedfordshire |
| Department | Department of Life Sciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Spectroscopic studies |
| Collaborator Contribution | Sample provision |
| Impact | We are actively studying tropomyosin, mutations in which are associated with the disease Familial Hypertrophic Cardiomyopathy (FHC). An abstract has been published to date Talks at international meetings Papers are in preparation |
| Start Year | 2009 |
| Title | 2Struc |
| Description | Examination of a query entry, being a protein atomic structure, and presenting from it the results from eight different packages describing different ways of evaluating the secondary structure contents. A second component is a comparison package between two (more in NMR models) protein structures identifying the similarities and differences between features in these structures. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2012 |
| Impact | The tool is being cited as being used regularly |
| URL | http://2struc.cryst.bbk.ac.uk/ |
| Title | Dichromatch |
| Description | Presents six different ways of evaluting the closest matching (three in each case) Circular Dichroism spectra in a given Refence set of spectra (default is those in the Protein Circular Dichroism Data Bank). |
| Type Of Technology | Webtool/Application |
| Year Produced | 2012 |
| Impact | A number if hits were made on this site (which at the time of writing is undergoing maitainance). |
| URL | http://dichromatch.cryst.bbk.ac.uk/ |
| Description | Brazil-Int-Exch |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was an intitiation meeting for collaborations with Brazil. Guests included the Brazillian Ambassador, the Brazillian Science Attache, the UK Head of Science Without Borders and BBSRC staff were also in attendance. This meeting generated a lot of enthusiasm for collaborative projects centred around circular dichroism and synchrotron radiation circular dichroism spectroscopy and has become the progenitor for a formal application being made for the creation of an SRCD beamline on the Brazillian Synchrotron at Campinas. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Chiao Tung, Taiwan |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was one of two research talks promoting the use of Synchrotron Radiation Circular Dichroism Spectroscopy across Taiwan in 2010 |
| Year(s) Of Engagement Activity | 2010 |
| Description | ECCB 2014 Workshop |
| 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 | I organised this workshop which was selected to be part of the 13th European Conference on Computational Biology. This was entitled as a "Workshop on Informatics Based Approaches for Circular Dichroism Data", and was specifically aimed at widening the audience interest in CD and particularly those with a computational bias aiming to stimulating their interest in the field. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Eu/UK CD/SRCD Workshop (Now part of the Warwick Analytical Sciences Workshop) |
| 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 | Numerous attendees have now become regular users of Circular Dichroism and Synchrotron Radiation Circular Dichroism as a result of the training they have received Some short-term collaborative projects have been instigated as a result of these workshops |
| Year(s) Of Engagement Activity | Pre-2006,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016 |
| URL | http://www2.warwick.ac.uk/fac/sci/wcas/events/analytical_sciences_summer_school_winter_workshop/ |
| Description | Int Workshop, Japan |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was one of a series of research talks promoting the use of Synchrotron Radiation Circular Dichroism Spectroscopy across Japan in 2010 |
| Year(s) Of Engagement Activity | 2010 |
| Description | Open Days (QM) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Schools |
| Results and Impact | Primarily science presentations at Open Days at QM and this did indeed spark questions and interest from those that assembled to watch the demonstrations I have no direct knowledge of impact from my presentations, but interest in studying in our School at QM has been rising steadily recently (but I cannot attribute this to my involvement!!) |
| Year(s) Of Engagement Activity | 2008,2009,2010,2011,2012,2013,2014 |
| Description | Osaka University |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This was one of a series of research talks promoting the use of Synchrotron Radiation Circular Dichroism Spectroscopy across Japan in 2010 |
| Year(s) Of Engagement Activity | 2010 |
| Description | QM Dental |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | This was an introductory talk showing how synchrotron radiation circular dichroism can be used to obtain exciting and novel results with increased information content. |
| Year(s) Of Engagement Activity | 2012 |
| Description | Riken Institute, Japan |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This was one of a series of research talks promoting the use of Synchrotron Radiation Circular Dichroism Spectroscopy across Japan in 2010 |
| Year(s) Of Engagement Activity | 2010 |
| Description | The Pet - Nature Futures |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | This was a science fiction feature in Nature and was aimed to stimulate the reader without being too deep in concept. The aims were to provide an interesting and novel way for the general reader to have an overview of how neural networks were utilised (without them being bombarded with heavy detail). Many who have read the article and contacted me have enjoyed it and not found the subject "heavy going". Those I know who have read the article have enjoyed the story, and have actually gained some overview knowledge of neural networks without being "hit" with the data !! |
| Year(s) Of Engagement Activity | 2009 |
| URL | http://www.nature.com/nature/journal/v461/n7261/full/461304a.html |
| Description | Tokyo University |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This was one of a series of research talks promoting the use of Synchrotron Radiation Circular Dichroism Spectroscopy across Japan in 2010 |
| Year(s) Of Engagement Activity | 2010 |
| Description | Tsung Hua, Taiwan |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was one of two research talks promoting the use of Synchrotron Radiation Circular Dichroism Spectroscopy across Taiwan in 2010 |
| Year(s) Of Engagement Activity | 2010 |