title: Effective optimization algorithms for fragment-assembly based protein structure prediction.
abstract: Despite recent developments in protein structure prediction, an accurate new fold prediction algorithm remains elusive. One of the challenges facing current techniques is the size and complexity of the space containing possible structures for a query sequence. Traditionally, to explore this space fragment assembly approaches to new fold prediction have used stochastic optimization techniques. Here, we examine deterministic algorithms for optimizing scoring functions in protein structure prediction. Two previously unused techniques are applied to the problem, called the Greedy algorithm and the Hill-climbing (HC) algorithm. The main difference between the two is that the latter implements a technique to overcome local minima. Experiments on a diverse set of 276 proteins show that the HC algorithms consistently outperform existing approaches based on Simulated Annealing optimization (a traditional stochastic technique) in optimizing the root mean squared deviation between native and working structures.
authors.affiliation: Department of Computer Science & Engineering, Digital Technology Center, Army HPC Research Center, University of Minnesota, Minneapolis, MN 55455, USA. deronne@cs.umn.edu
authors.forename: Kevin W
authors.initials: KW
authors.lastname: Deronne
authors.forename: George
authors.initials: G
authors.lastname: Karypis
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008956:Models, Chemical; D008969:Molecular Sequence Data; D010449:Peptide Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D011786:Quality Control; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins