FibSim, a web application to refine fibrillar macromolecular models : Masters thesis in Bioinformatics

Fibrillar macromolecules are long, linear structures that have helical symmetry. A technique called X-ray fiber diffraction (XRFD) is often used to help solve the three-dimensional structure of fibrillar macromolecules. Models of fibrillar structure, built de novo, using homologs or using experimental data derived from other methods should be compared to this experimental XRFD data to test and refine the models. To facilitate this comparison, software has been developed to simulate XRFD data from fibrillar models, which is then compared to the experimental data. However, currently this process often involves a few independent programs. A new program has recently been developed that, in one package, generates simulated XRFD data from the model and compares it statistically to the experimental XFRD data, if included in the simulation. The outcome of the statistical test can then be used to guide the refinement of the model. This package also uses an algorithm that utilizes ‘simultaneous model building’ to improve predictions. Currently, this software is server-bound, computationally intensive and has minimalistic, command-line functionality. As a means to publically share this unique program, I present FibSim, a web server for this fibrillar refinement program. FibSim provides the model-refinement functionality of the original software with an easy-to-use graphical user interface.