title: Designing succinct structural alphabets.
abstract: BACKGROUND
  The 3D structure of a protein sequence can be assembled from the substructures corresponding to small segments of this sequence. For each small sequence segment, there are only a few more likely substructures. We call them the 'structural alphabet' for this segment. Classical approaches such as ROSETTA used sequence profile and secondary structure information, to predict structural fragments. In contrast, we utilize more structural information, such as solvent accessibility and contact capacity, for finding structural fragments.
  
  
  RESULTS
  Integer linear programming technique is applied to derive the best combination of these sequence and structural information items. This approach generates significantly more accurate and succinct structural alphabets with more than 50% improvement over the previous accuracies. With these novel structural alphabets, we are able to construct more accurate protein structures than the state-of-art ab initio protein structure prediction programs such as ROSETTA. We are also able to reduce the Kolodny's library size by a factor of 8, at the same accuracy.
  
  
  BACKGROUND
  The online FRazor server is under construction.
authors.affiliation: David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ont. N2L 3G1, Canada. scli@uwaterloo.ca
authors.forename: Shuai Cheng
authors.initials: SC
authors.lastname: Li
authors.forename: Dongbo
authors.initials: D
authors.lastname: Bu
authors.forename: Xin
authors.initials: X
authors.lastname: Gao
authors.forename: Jinbo
authors.initials: J
authors.lastname: Xu
authors.forename: Ming
authors.initials: M
authors.lastname: Li
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins