View Proposal #155
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| ID | 155 |
|---|---|
| First Name | Di |
| Last Name | Wu |
| Institution | Iowa State University |
| Speaker Category | graduate student |
| Title of Talk | Protein Structure Determination: A Rigid Geometric Build-up Algorithm for Solving a Distance Geometry Problem with Sparse Exact Distance Data |
| Abstract | Protein Structure Determination: A Rigid Geometric Build-up Algorithm for Solving a Distance Geometry Problem with Sparse Exact Distance Data Di Wu and Zhijun Wu Program on Bioinformatics and Computational Biology Department of Mathematics Iowa State University Ames, Iowa 50011 Abstract. Given a set of distances for certain pairs of atoms in a protein, the coordinates of the atoms and hence the protein structure can then be determined through solving a so-called distance geometry problem. However, it has been proved to be a NP hard problem when only a set of partial distances given. Previously, we used a so-called geometric build-up approach to develop several algorithms for solving the distance geometry problem with a set of sparse distance data. In this method, the coordinates of the atoms in a protein are determined as one atom at a time, with the distances from four base atoms to the atom to be determined. However, the requirement for four base atoms for the unique determination of each atom is sufficient, but unnecessary and even redundant for rigid structural determination. Here we investigate a rigid geometric build-up algorithm, which requires three base atoms instead of four base atoms for the determination of each atom. It could generate rigid structures, even a unique structure for very sparse distance data of a protein eventually. Due to the reflection in the determination for some atoms, this algorithm may also produce multiple structures satisfying given distances. We present the results obtained by using the algorithm for the determination of the structures, which suggests the potential of applying the algorithm to the distance based protein structural modeling. |
| Subject area(s) | Computational Biology and Applied Mathematics |
| Suitable for undergraduates? | Yes |
| Day Preference | |
| Computer Needed? | Y |
| Bringing a laptop? | Y |
| Overhead Needed? | Y |
| Software requests | MS Powerpoint |
| Special Needs | |
| Date Submitted | 2/28/2006 |
| Year | 2006 |