Home > Archives > Jonathan M. Dugan   Jonathan M. Dugan Stanford Using Surface Envelopes in 3D Structure Modeling Modeling the 3D structure of biomolecules assists in the understanding of diseases and normal biological processes, and in the discovery of novel pharmaceuticals. Current crystallographic methods for the determination of these structures have been very successful, but are not applicable for all cases. Fortunately, other experimental methods can provide useful evidence regarding biomolecular structure, although typically these data are noisy and sparse. The sources of these data include distances derived from NMR and other biochemical and biophysical experiments. For example, we can derive surface envelope (SE) data from cryo-electron microscopy, binding or affinity measurements, predictions, or homology modeling. This talk outlines the development and implementation of algorithms capable of integrating SE data into the 3D structure modeling process. I present the results of modeling several proteins and test structures with distance data and SE data derived from solved molecular structures. I also present a computational platform, called GRAPE (General Replaceable Atomic Position Engine) that provides unified data structures and algorithms that are highly flexible and applicable to a variety of different data types -- with the goal of combining these heterogeneous data sources to maximize their utility in modeling macromolecular structures. Bio: Jon is working on his PhD at Stanford University, and should be done around May 2002. His research interests include bioinformatics and structural biology. His thesis work involves the creation of novel algorithms to combine different data sources to create high resolution structural models of biomolecules. Prior to his work at Stanford, Jon worked for 3 years at the M. D. Anderson Cancer Center in Houston as a medical physicist, where he concurrently earned his MS from the University of Texas. He also has an A.B. in Chemistry and Physics from Bowdoin College.
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