Algorithmic research problems in molecular bioinformatics

The large amounts of data being assembled in the genome sequencing projects provide a grand challenge to science, namely their interpretation. There are several aspects to this interpretation such as identifying genes, determining the structure of the encoded proteins, discovering the mechanisms, by which proteins execute their biological function, and gaining insights into what role noncoding regions of the DNA play in gene regularization and expression, as well as metabolism. Due to the increased computing power and, especially, due to sophisticated graphics technology, one can visualize the structure and dynamics of molecules on the computer screen. What is still largely missing is a set of reliable models and algorithmic methods for deriving molecular structures on the basis of sequence data, as well as methods for the reliable prediction and analysis of interactions between biomolecules such as enzymes and their substrates. The author points out a few problems for which careful modeling and the development of appropriate algorithmic techniques is at the center of progress in computer-aided molecular biology