Enhancements to ProFit

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This project will make a number of enhancements to the computer software known as ProFit previously written by the applicant for comparing sets of protein or RNA coordinates. These enhancements are largely requested by current users and will enable additional applications and research. The optimal 'fitting' of two or more sets of protein or RNA coordinates is a fundamental requirement for examining structural similarity and variability. This fitting is done when predicting the three-dimensional structure of proteins based on other known structures and in evaluating the performance of modelling methods. It is also used in studying the variability and flexibility of protein and RNA structures. This is useful when a single molecule is flexible and when one wishes to examine the effects of mutations or different bound ligands on protein structure. Fitting is also used to examine the variability of related protein structures to study evolution or protein structures. ProFit is a very widely used program for fitting two or more protein or RNA structures. A set of equivalent atoms in the structures must be specified, but ProFit also allows the equivalent atoms to be optimized automatically. Once the structures have been fitted, a simple statistic known as the 'root mean square deviation' (RMSd) is calculated to give an indication of the similarity. The work proposed in this project will provide a number of enhancements to the program. Most importantly, a number of additions requested by users will be implemented which include removing restrictions when dealing with structures having more than one poly-peptide chain. This is becoming particularly important as crystallographers are now able to solve enormously complex structures. We will also perform some internal cleanup of the code to make it more maintainable and will provide a Windows version and a web-based graphical interface to improve the usability of the software for Biologists.