title: Ab initio protein structure prediction using a combined hierarchical approach.
abstract: As part of the third Critical Assessment of Structure Prediction meeting (CASP3), we predict the three-dimensional structures for 13 proteins using a hierarchical approach. First, all possible compact conformations of a protein sequence are enumerated using a highly simplified tetrahedral lattice model. We select a large subset of these conformations using a lattice-based scoring function and build detailed all-atom models incorporating predicted secondary structure. A combined all-atom knowledge-based scoring function is then used to select three smaller subsets from these all-atom models. Finally, a consensus-based distance geometry procedure is used to generate the best conformations from each of the all-atom subsets. With this method, we are able to predict the global topology/shape for all or a large part of the sequence for six out of the thirteen proteins. For two other proteins, the topology/shape for shorter fragments are predicted. This represents a marked improvement in ab initio prediction since CASP was first instigated in 1994.
authors.affiliation: Department of Structural Biology, Stanford University School of Medicine 94305, USA. ram@zen.stanford.edu
authors.forename: R
authors.initials: R
authors.lastname: Samudrala
authors.forename: Y
authors.initials: Y
authors.lastname: Xia
authors.forename: E
authors.initials: E
authors.lastname: Huang
authors.forename: M
authors.initials: M
authors.lastname: Levitt
mesh_terms: D000465:Algorithms; D020407:Internet; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins