Bruce S. Duncan

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One of the challenges in biocomputing is to enable the efficient use of a wide variety of fast-evolving computational methods to simulate, analyze, and understand the complex properties and interactions of molecular systems. Our laboratory investigates several areas including molecular visualization, protein-ligand docking, protein-protein docking,(More)
PROTEAN is an evolving knowledge-based system that is intended to identify the three-dimensional conformations of proteins in solution. Using a variety of empirically derived constraints, PROTEAN must identify legal positions for each of a protein's constituent structures (e.g., atoms, amino acids, helices) in three-dimensional space. In fact, because(More)
The description of molecular shape is important in the analysis of protein-protein and protein-ligand interactions. We describe volumetric and surface-based techniques for computing shape properties of molecular surfaces. The surface is defined as an isocontour of an approximate electron density function. Each technique can compute several scalar and vector(More)
A method is described for determining the family of protein structures compatible with solution data obtained primarily from nuclear magnetic resonance (NMR) spectroscopy. Starting with all possible conformations, the method systematically excludes conformations until the remaining structures are only those compatible with the data. The apparent(More)
Nuclear Overhauser Enhancement Spectroscopy (NOESY) is a powerful NMR technique for obtaining structural information on proteins in solution. 2DFT NOESY experiments readily provide information on dipole coupled protons, an indication of close spatial proximity. Unfortunately, quantitative interpretation of NOE measurements in terms of molecular structure is(More)
The problem of arranging a set of physical objects according to a set of constraints is formulated as a geometric constraint satisfaction problem (GCSP), in which the variables are the objects, the possible locations of the objects are the possible values for the variables, and the constraints are geometric constraints between the objects. A GCSP is a type(More)
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