Award details

Crystallographic methods and software development in a high-throughput environment

Reference	BB/D522403/1
Principal Investigator / Supervisor	Professor Kevin Cowtan
Co-Investigators / Co-Supervisors	Dr Garib Murshudov, Professor Keith Wilson
Institution	University of York
Department	Chemistry
Funding type	Research
Value (£)	440,036
Status	Completed
Type	Research Grant
Start date	01/12/2005
End date	30/04/2009
Duration	41 months

Abstract

The plans are as follows: Task 1: Molecular Replacement (MR). 1) Implement communication tools using xml tags and test as a proof of principle for automated MR. 2) Improve analysis of the crystal contents to find out if there are several molecules and if so to use the self rotation function to decide if multimers are present. Then use this information in the decision making procedure during MR. 3) analyse the PDB for intensity curves, find the optimal curve to describe the current experiment and use it to derive normalisation coefficients. Task 2: COOT: 1) Implement fully automated model building using both fast methods and intensive methods. Fast methods will be used from within the COOT graphical model building software, and intensive methods within automated procedures. 2) Improve automated rebuilding tools in COOT for MR and binding study problems, and implement stand-alone versions. Initial tools for automated rebuilding in MR should have been released by the start of the grant, however automated loop rebuilding and iteration with phase improvement will require further work. 3) Fill in the remaining gaps in the functionality of the COOT graphical model building software to allow it to become a full, free and modern replacement for existing software. This includes various manual and assisted model building tools and user interface improvements. Task 3: Web Services: 1) Set up a parallel cluster with suitable security for web-accessible computational problems. A registration system will be employed to allow free access to academic users, using grid certificates or other authentication tokens. Automated molecular replacement software will be deployed as a proof of concept. 2) A massive molecular replacement application will be implemented around the automated MR application. The MR search will be performed in parallel over several nodes, and will be extended as the grant progresses to include the automated refinement and data and model evaluation steps developed for the first task. 3) Extend this approach to the use of smaller fragments, derived from further analysis of the PDB, as developments in the MR software make this possible.

Summary

The aim is to improve the software tools used in studying structure of the molecules which make up living organisms. All living organisms are made up of complex biological molecules. These molecules are described by a blueprint, which is in the form of a DNA code describing how to make the molecules. A number of projects, including the Human Genome Project, have deciphered many of these codes. We can therefore read the plans for many of the molecules of life. However without a knowledge of the 3D structure of the molecules, it is very hard to understand what they do. Understanding what they do is a first step in fixing them when they go wrong, and therefore, in curing a range of illnesses. The approach to this problem is through Structural Biology, in which the molecules are manufactured from their blueprints and 3D models are constructed for them usually using X-ray crystallography. This allows pictures to be made of biological molecules in which individual atoms can be identified. Once the 3D structure is known, it is often possible to make deductions about the function of the molecule. Structure solution by X-ray crystallography requires a number of complex experiments followed by complex computation and problem solving by experienced scientists. We aim to improve some of the computational tools to make this task easier and more automatic, and to allow the solution of more difficult problems. In particular, the problem is broken down as follows: 1) Producing the biological molecules from their DNA blueprints. 2) Growing regular crystals which can be used in an X-ray experiment. 3) Illuminating the crystals in an X-ray beam, and measuring the X-rays scattered. Only part of the scattered information can be measured (the intensities), the critical phase information is lost. 4) Estimating the missing phase information using multiple experiments or previously known similar structures. Using this information, an approximate (essentially a blurred) image of the moleculeis generated. 5) Making an initial interpretation of this image in terms of the biological building bricks of the molecule, in the case of a protein the amino acids. 6) Refining the initial 3D model to give the best fit to the data which makes physical and chemical sense. 7) Evaluating the model to obtain a good indication of how reliable it is. This project is concerned with improving the software used in the final three steps, which traditionally involve a significant amount of user intervention, although automated methods are now available for easier cases. We have already developed good tools for assisting the user in making the additional interpretation, and propose to provide further assistance for non-expert users, and automated tools for laboratories where many structures are being solved simultaneously. We also propose to provide a tool that would make future structure solution easier. In other words we want to provide such a tool that can use already available solved structures. In the final stages of structure solution it is desirable to know if the solved structure is correct. This can be done either using tools that can analyse the internal consistency of the structure or tools that can use information not used in the structure solution (external consistency). Finally, we would like to provide a range of world-wide-web based services, to allow users to try the very latest software on their difficult problems without having to down load the latest, and least tested, software. This will allow users from small labs without high-performance computing facilities to perform some longer and more demanding calculations.

Committee	Closed Committee - Biomolecular Sciences (BMS)
Research Topics	Structural Biology, Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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