Algorithms for the Building of Model Proteins Using Structural Homology

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Further development of an interactive software product to aid in the building of model proteins is proposed. Dr. Lee proposes to refine, incorporate, and test four new algorithms in the program. The first is the incorporation of secondary structure information into the algorithm for the automatic locations of conserved regions in the proteins. It will prevent inappropriate sections of the reference proteins from being classified as being conserved. The second is the adding of a method for generating loops in the variable regions. They will be more random in nature than those currently found in a structural database, and will span more of conformational space. The third is an algorithm for systematically searching possible conformations for side chains. It will help find a set of self-consistent rotamers that pack well. The fourth is an algorithm to incorporate low resolution crystal data into the model. It uses simulated annealing using x-carbon coordinates as distance constraints to find a folded protein conformation with little input structural information. It can also be applied in a more limited way as an adjunct to other model building methods. Taken together, these new methods will be of great use to the researchers who use the software product.