Enhancing the Phyre2 protein modelling portal for the community

Proteins are large molecules that are the machinery of life. They are long chains of different components and the order of these components is the amino-acid sequence. The genome projects are now determining the sequences of proteins from many species including plants, animals and microbes. Experimental methods can reveal the 3D structure of a protein, and this information is central to basic biological understanding and the exploitation of this biological knowledge has major implications for improvements in agriculture, animal welfare, health, and biotechnology. However, generally this essential information is not available from experiment. Biologists then require computational methods to predict this information.

The Sternberg group has developed a powerful and user-friendly resource for predicting the 3D structure of a protein from its sequence. The first version was 3D-PSSM and the more recent versions are Phyre and Phyre2. This is disseminated via a web server - a user pastes their protein sequence of interest into a box and the server returns details of the predicted 3D structure with atomic coordinates and additional information. This resource has proved exceptionally popular with the world-wide scientific community. There have been over 1.5 million sequence submissions to these servers and over 3,700 literature citations to the three main papers describing 3D-PSSM and Phyre. There are 60 papers citing the use of Phyre2 for their research which have been published in the highly-prestigious journals of Nature, Science and Proceedings of the National Academy of Sciences, USA.

Users of Phyre2 are supported by help pages, a video tutorial and e-mail help from us. Recently we contacted our users and we obtained over 1,000 letters of support demonstrating the value the community places on Phyre2. Based on our e-mail correspondence and information within these letters of support we identified a series of enhancements we wish to make to the Phyre2 web site. This grant will provide support for us to maintain, support and enhance the Phyre2 web server for use by the community. Specifically we propose:

1) To ensure the Phyre2 portal remains up to date and robust, provides a fast turnaround, and is supported by assistance to users.
2) To enhance user support by the development of extensive training material (with case studies), the provision of video help dynamically linked to every output web page and by contributing to national, European and world-wide activities in training.
3) To promote the widest use of Phyre2 by the bioscience community.
4) To disseminate the Phyre2 portal via publication, national and international conference presentations, and the provision of training workshops at different sites in the UK.
5) To enhance the modelling by ensuring Phyre2 incorporates the very latest modelling components which are available.
6) To enable large scale analyses of genomes including the provision of a fast processing facility using computing resources that can be purchased by any user (known as cloud computing).
7) To predict where on a protein certain biological features might occur and which regions of the protein may bind small molecules which are relevant to protein function.
8) To develop an exciting and novel approach, LogPhyre, to forge collaborations between Phyre2 users who are studying similar regions of protein space. LogPhyre will ensure user confidentiality and will, with user agreement, broker connections between users.
9) To participate in international comparative evaluations of protein structure prediction, known as CASP and CAMEO.
10) To work with our scientific management board to ensure we meet our objectives and are responsive the needs of our diverse user base.
11) To engage with diverse stakeholders including policy makers, museums, the general public and especially young people.

Phyre2 is a widely-used web portal for protein structure prediction server. It is used by tens of thousands of users worldwide due to its power, functionality and a user interface that is informative and easy to use for biologists. A user pastes their protein sequence of interest into a box and the server returns details of the predicted 3D structure with atomic coordinates and additional information. Phyre2 and its predecessors have processed over 1.5 M sequences and have had over 3,700 citations. Recently we contacted our users and we obtained over 1,000 letters of support. Based on user feedback we identified enhancements we wish to make to Phyre2. Our aims are:
1) To ensure the Phyre2 portal remains up to date, robust and provides a fast turnaround.
2) To enhance user support by the development of extensive training material (with case studies), the provision of video help dynamically linked to every output web page and by contributing to national, European and world-wide activities in training.
3) To promote the widest use of Phyre2 by the bioscience community.
4) To disseminate the Phyre2 portal via publication, conference presentations, and the provision of training workshops.
5) To enhance the modelling by ensuring Phyre2 incorporates the very latest modelling components.
6) To introduce additional modelling features including template selection, model clustering, refinement using Rosetta, linking to the Cn3D viewer, and integrating with the popular Jalview sequence modelling tool.
7) To enable large scale analyses of genomes including the provision of a fast cloud batch procedure.
8) To predict post-translational modifications and ligand binding-sites.
9) To participate in the CASP and CAMEO international comparative evaluations of structure prediction.
10) To work with our management board to ensure we are responsive the needs of our users.
11) To engage with policy makers, museums, the general public and especially young people.

This proposal is to maintain and enhance a web-based bioinformatics resource for the bioscience community to perform protein structure prediction using our Phyre2 system. Based on current demand and anticipated growth we envisage supporting at least 200,000 different users over the course of the five years. We will now identify those groups that will benefit from this research and in what way they will benefit.

Academic - Many of the users of the Phyre2 resource will be academic groups and the results of their use of Phyre2 will advance their research leading to economic and social benefit. Our current user-base is international and spans diverse researchers in bioscience who require information about protein structure and function. Feedback from users has shown that a Phyre2 prediction can have a transformative effect on their research moving their conceptualisation into detailed consideration of the molecule at the three-dimensional atomic level. There are numerous application areas. One major application area is the identification of novel targets for pharmaceutical intervention. Structure guides both the design of small molecules and bio-therapeutics, such as monoclonal antibodies. The consequence of the design of novel pharmaceuticals has clear health and commercial benefit. A second application area is the agricultural sector. Similar considerations apply to animal health as for the pharmaceutical industry. In addition, genome information can be helpful in selective breeding of crops and fruit. The biotechnology and bio-energy sectors can focus on the modification of biological pathways and information about the structure and function of genes can inform these studies.

Public sector - Agencies involved in public health and food security are expected to continue to use the Phyre2 portal. For example the location of a mutation on the surface of a human, animal or plant pathogen could be mapped to provide insight into structure/function relationships. This will impact on health and well-being.

Policy makers and the general public - Via open days at Imperial College, members of the general public will see demonstrations of Phyre2. This will highlight an area of research - bioinformatics - of which they may not have been aware. Furthermore this will demonstrate the collaborative nature of scientific research with its implications of value for money.
In particular the Imperial Festival is an annual event which attracted over 10,000 in 2013. From the policy side, Imperial invites to the Festival representatives from professional membership bodies, local and central government, higher education bodies including other university senior staff, and research funders. We will continue to give invited lectures to groups other than researchers. Previously, Prof Sternberg has addressed the Prince's Trust and a meeting at Brighton linking Art and Science.

Schools - In talks to schools by the PI, the Phyre2 server is described as a web-based resource for use by the community. This always has a major impact on the audience. Students are impressed by the Phyre2 usage figure - over 1.5 million hits - which is placed in the perspective of popular YouTube clips shown on TV programmes that often have fewer hits. The opportunity to develop a resource used by so many other scientists excites students as a highly worthwhile activity.
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