Surface feature characterization and expression analysis of protein interactions

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High-throughput proteomics experiments and structural genomics efforts are generating a huge amount of interaction and structural data, but it will not be feasible or possible to characterize all biomolecular interactions at the level of structure. Effective means of modeling will be required for the majority of interactions of interest. The proposed research will develop methods to effectively model a target group of protein-protein interactions, and has the larger goal of developing methods for predicting any interaction. Many protein-protein interactions are mediated by one structure recognizing a particular peptide sequence, often in a loop or unstructured region of the second protein. If this is the case, a recognition method that can dock a structured protein to an unstructured region will be needed to identify many relevant biological interactions. The proposed research addresses this problem.