Maintaining and extending PHYRE2 to deliver an internationally-recognised resource for protein model

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 human, 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 version is known as Phyre. 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 highly popular with the community. There have been over 750,000 submissions and the current rate is 2,500 per week. There have been over 2,000 citations to the three main papers describing 3D-PSSM and Phyre.

However, genes and their protein products do not act in isolation. The rapidly growing field of Systems Biology aims to understand Biology at the level of complex systems of interactions, of which proteins are a central component. Many techniques have recently become available to predict the vital parts of a protein that confer its function and the regions of a protein that take part in interactions with other molecules in the cell. Modelling these regions permits a better understanding of the role of genetics in disease by elucidating their role in the basic biochemistry of the cell and the network of interactions in which they take part.

This grant will provide support for us to maintain, support the Phyre web server. We will provide e-mail user support together with extensive documentation. In addition, we will run three hands-on workshops and four road-shows across the UK for biologists interested in using the methodology. The work will be disseminated by publications in the scientific literature and presentations at national and international meetings.

The functionality of Phyre will be enhanced to support the following topics.

1) The prediction of the interacting partners of a protein in the cell to better elucidate function. Determining the interactions a protein makes with other proteins is critical for a researcher to elucidate the protein/gene's wider role in cellular processes and disease. It can aid researchers in building larger models of entire systems.

2) The modelling of the structure of multiple proteins in a complex. In addition to determining which proteins are interacting ((1) above), the specific nature of that interaction gives researchers a detailed insight into which parts of a protein are critical for the interaction. This can then guide hypotheses and experimental design.

3) To suggest the effects of mutations on the structure and function of the protein. Algorithms are available to predict whether a mutation in a protein is likely to alter its function in the cell and these advances will be incorporated into the server.

5) To provide enhanced visualisation, which is key when dealing with complex three-dimensional protein structure. We will substantially extend the user's ability to plot a variety of predicted features mapped onto 3D model predictions, in particular functionally important parts of the protein and regions where mutations are known to occur.

Phyre, our protein structure prediction server, is used by hundreds of groups worldwide. The aim of this proposal is to maintain, support and extend Phyre to include the prediction of protein interactions, functional sites and multi-protein complexes. We propose to:

1) Hold 3 workshops and 4 road-shows around the UK, maintain the server, provide full user-support and integrate new developments in the field as they arise.

2) Take part in the internation blind trial of protein structure prediction (CASP).

3) Integrate freely available tools and databases for the prediction of protein interfaces (e.g. SCOPPI, ProtInDB). Couple interface prediction of two user proteins to the freely available iWrap interface threading algorithm. Add the ability to return a predicted Biological Unit (BU) for homo-oligomers using both the existing PDB biomolecule information and the complementary ProtBud database of BUs. Potential clashes will be resolved using the method described in (2).

4) Extend our Poing multiple template modelling tool to handle multiple protein chains. Using existing homologous complexes to derive distance constraints, we will be able to relieve clashes and utilise multiple homologous complex constraints simultaneously.

5) Predict interacting partners by combining the remote homology detection of Phyre with the STRING database of interacting proteins via their existing API. A confident template structure detected by Phyre will be used to detect close homologues of the template in STRING to provide candidate interaction partners for the user protein including template structures in complexes.

This proposal is to maintain and enhance a web-based bioinformatics resource for the bioscience and biomedical communities to perform protein structure prediction using our Phyre system. Based on current demand and anticipated growth we envisage supporting over 20,000 users over the course of the three 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 Phyre resource will be academic groups and the results of their use of Phyre will advance their research leading to economic and social benefit. Our current user-base is international. The current user-base spans a diverse section of researchers in bioscience and biomedicine requiring information about protein structure and function. Feedback from users has shown that a Phyre 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 bio-energy sector 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 Phyre server. 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.

Schools - In talks to schools by the PI, the Phyre server is described as a web-based resource. The development of tools used by many other researchers illustrates the broad impact of science research to the students.

General public - Via open days at Imperial, members of the general public will see demonstrations of Phyre. This will highlight an area of research - bioinformatics- which they may not have been aware of. Furthermore this will highlight the collaborative nature of scientific research with its implications of value for money.