Automating the Determination of 3d Protein Structure 3.2 Databases 3.3 New Method of Determining Structural Similarity 4 Integrating a Database: Dbemp

Abstract

The creation of an automated method for determining 3D protein structure would be invaluable to the eld of biology and presents an interesting challenge to computer science. Unfortunately , given the current level of protein knowledge, a completely automated solution method is not yet feasible; therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the rst step toward designing a program to determine protein conformation automatically. The properties of a protein are largely determined by its three-dimensional structure Voet and Voet 1990]. This statement would seem to simplify the process of understanding proteins and their functions. Actually, it exposes the major reason that so little is really understood about speciic proteins or even proteins in general. For many proteins, certain properties of their function can be described, but no explanation of how they function can be given. The result is a gaping hole in our understanding of the fundamental processes of life. Nothing in the cell remains unaaected or unprocessed by proteins in some way. Many of the structural components of the cell are proteins; and, perhaps more important, proteins lie at the heart of the biological reactions that occur within the cell. Most objects known to have catalytic activity contain proteins, whether the protein is an enzyme and responsible itself for the catalysis or is the structural component of ribozymes. An understanding of proteins would unravel most, if not all, the processes necessary to regulate and sustain life. Such an understanding would open new doors in medicine, industry, agriculture, pharmaceuticals, and many other areas. The determination of protein structure is a nontrivial problem. Much of the necessary information about which structure a protein will fold into is contained in the linear sequence of amino acids; therefore, it may be possible to determine the 3D structure of a protein from its amino acid sequence. Many scientists are currently working toward such an understanding, but to date, the mechanisms and rules by which a protein folds remain elusive. Key to current research are crystallographic techniques , which provide electron density maps that provide incomplete, but highly informative, data …

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Cite this paper

@inproceedings{Rayly2011AutomatingTD, title={Automating the Determination of 3d Protein Structure 3.2 Databases 3.3 New Method of Determining Structural Similarity 4 Integrating a Database: Dbemp}, author={Karen D. Rayly and Terry Gaasterland}, year={2011} }