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Rapid protein structure determination relies greatly on the availability of software that can automatically generate a protein model from an experimental electron density map. Tremendous advances in this area have been achieved recently. In favorable cases, existing software build over 90% of the final model. But in less favorable cases (medium-low resolution), 2/3 completeness is obtained. Manual completion is particularly difficult and time consuming. Our goal is to develop automatic tools to fill the missing gaps (or loops) in the models. This work is being conducted in close cooperation with Dr. Henry van den Bedem and Dr. Ashley Deacon at the Joint Center for Structural Genomics, Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center.