Developing software for protein analysis
The project 'Automated NMR structure-based assignments' (NMR-SBA) focused on problems in reading the spectra from nuclear magnetic resonance (NMR) studies. Researchers addressed this task by developing automated NMR structure-based assignment software. To reach this goal, several milestones had to be reached. These included developing algorithms for analysing proteins of various sizes and testing the algorithms to determine the best parameters for their use. In addition, the team incorporated new types of NMR data into the software to increase its usability. They also extracted more data from existing sources to enhance the performance of the algorithms. The team developed three algorithms and corresponding software to tackle the assignment of proteins in the presence of a template. Researchers used algorithms based on an existing framework called nuclear vector replacement (NVR). The first of these approaches, NVR-BIP, used binary integer programming (BIP) to find the exact solution for minimizing the size of the proteins. This technique improved the assignment accuracy of the NVR tool significantly. However, it didn't solve the problem for large proteins. Therefore, the team developed two other algorithms for these large proteins. In addition, new data, which previously had to be set manually, have been incorporated into the software. Researchers used data from public databases, as well as data provided by the team's collaborators, to test the software. If a particular data type was not available, they used synthetic data. Toward the end of the project, the team received a grant to work with high-profile scientists on new therapeutic avenues. The software will contribute to the study of large proteins for the development of new antibiotics against antibiotic-resistant gram-negative bacteria. This is one of many ways that scientists can take advantage of this software. Many more will probably be discovered in the future.
