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UK funding (£633,870): The Dundee Resource for Protein Structure Prediction and Sequence Analysis Ukri1 Mar 2013 UK Research and Innovation, United Kingdom
Overview
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The Dundee Resource for Protein Structure Prediction and Sequence Analysis
| Abstract | This resource application is focused on supporting and maintaining computer tools and techniques developed at the University of Dundee that are in daily use by thousands of biological scientists throughout the UK and the world. The resource will not only ensure that these tools are readily available to all scientists, but also improve the ability of scientists and students to use them through better interfaces and via regular face-to-face training courses and other on-line materials. The tools focus on the analysis of protein sequences and structures which are briefly introduced here. The plans to make a plant, animal or micro-organism are encoded as the molecule DNA and known as its genome. The genome can be represented as a long word made up of four different letters (A, C, G, T). The genome may be a few thousand letters long for a virus, to several billion letters for plants and animals. The genome is divided up into regions called genes which are translated by complex molecular machines into other molecules such as proteins. Humans and other animals have 20-30,000 genes that code for proteins and each protein made up of a sequence of 20 different amino acid types joined together in a chain. Protein sequences from an organism vary in length from a few amino acids, to several thousand and can be represented as a word made up of 20 different letter types. The protein chain folds up into a complex three-dimensional shape that is defined primarily by its sequence. The shape of the protein, its "conformation", dictates the biological function of the protein, so understanding the conformation of a protein is vitally important to understanding the protein function. Over recent years there have been huge advances in technology to sequence DNA and so the genomes of many different organisms have been determined. As a consequence, the sequences of several million proteins are now known but less than 100,000 have had their detailed three-dimensional structures worked out. The computational tools that will make up this resource help to bridge this information gap by classifying protein sequences and making predictions of protein structure that can guide biologists to design more efficient and effective experiments. The main objectives of the proposal are to provide support, maintenance and training for the popular JPred protein structure prediction server which performs up to 95,000 predictions monthly for scientists in 140 countries, the TarO protein sequence analysis suite and Kinomer protein kinase classifier and database. The new resource will integrate these individual tools with a consistent look-and-feel and make them available to researchers and tool developers in new ways over and above a conventional web site. Web sites are good for humans to interact with, but less useful for computer software to interface to. Since our tools are useful for large analyses that might be done on many thousands of proteins, the new resource will also support a novel "web services" interface to the tools. Web services allow a program or application to be run remotely from within a program. For example, I might have a program running on my desktop computer, but call for an intensive calculation to be done on a remote high-performance computer system. We have recently developed a new method to deploy web services (called JABAWS) that makes installation of web services straightforward. A key part of the new resource will be to add more complex applications such as structure prediction to Jabaws and so make them readily available to programmers and end-users |
| Category | Research Grant |
| Reference | BB/J019364/1 |
| Status | Closed |
| Funded period start | 01/03/2013 |
| Funded period end | 31/08/2018 |
| Funded value | £633,870.00 |
| Source | https://gtr.ukri.org/projects?ref=BB%2FJ019364%2F1 |
Participating Organisations
| University of Dundee | |
| UNIVERSITY OF OXFORD | |
| EMBL European Bioinformatics Institute (EMBL - EBI) | |
| Ecole Polytechnique | |
| Bristol-Myers Squibb | |
| Genentech, Inc |
The filing refers to a past date, and does not necessarily reflect the current state. The current state is available on the following page: University of Dundee, Dundee.
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