In work with faculty Wei Wang, Jans Prins, Alex Tropsha, and Jack Snoeyink, they tested different graph representations of protein structures, including Delaunay tessellation graphs, contact maps, and chose almost-Delaunay graphs as being robust in the presence of coordinate perturbations. They developed a fast method to generate maximal frequent subgraphs directly using a tree representation, ...

Since about 10 years ago, computer algorithms are available that can generate probable structures of molecular crystals [1]. Such predictions are important for virtually any scientific research and industrial application that deals with molecular crystals. The modified Monte-Carlo Simulated Annealing method [2] of PI Robert Gdanitz (NCAT, Physics) is, in fact, the first method that allows for a...

Robert Gdanitz, Senior Research Associate in the Department of Physics at North Carolina A&T State University, has been named a PI on the BioGeometry project effective June 2003. Robert is a theoretical physical chemist with expertise in developing electronic structures as well as force field methods. He interacts with group members at Chapel Hill, Duke, and Stanford to further develop his meth...

The second BioGeometry meeting of 2003 will take place at Duke University on Monday-Tuesday, November 17-18. PIs and students from the four participating institutions will attend, as will a representative from the NSF. Motivation: The problem of protein design is to construct an amino acid sequence that folds to a desired structure. PI Homme Hellinga (Duke Biochem) has had significant success i...

at Spelman College, worked with Pankaj Agarwal and Yusu Wang, who just completed her PhD, at Duke. Hillary’s summer project was about analyzing the performance of the algorithm developed at Duke to generate features on a molecular surface. The features are then used to predict good configurations for protein docking. For efficiency reasons, we would like to use as few features as possible. The ...

Background. Computing various descriptors of the extent of a set P of n points in Rd has found many useful applications in shape analysis, data mining and other areas. These descriptors, called extent measures, either compute statistics of P itself (e.g., diameter, width), or they compute statistics of a (possibly nonconvex) geometric shape (e.g., sphere, box, cylindrical shell) enclosing P. Al...

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Reconstruction of lower limb defects is quite challenging in terms of scarcity of locally available flaps, poor wound healing and need for prolonged immobilization. Normally also there is decreased blood supply in the anterolateral aspect of leg and foot. Leg and foot is like a peninsula with no distal tissues available for proximal reconstruction. Also there is a paucity of loose tissue in leg...

Multiple Sequence Alignment (MSA) is a central problem in computational molecular biology --it identifies and quantifies similarities among several protein or DNA sequences.The well-known dynamic programming (DP) algorithms align k sequences (each of length n) by constructing a k-dimensional grid graph of size O(nk), with each of the sequences enumerating one of the dimensions of the grid. The ...