title: Incorporation of local structural preference potential improves fold recognition.
abstract: Fold recognition, or threading, is a popular protein structure modeling approach that uses known structure templates to build structures for those of unknown. The key to the success of fold recognition methods lies in the proper integration of sequence, physiochemical and structural information. Here we introduce another type of information, local structural preference potentials of 3-residue and 9-residue fragments, for fold recognition. By combining the two local structural preference potentials with the widely used sequence profile, secondary structure information and hydrophobic score, we have developed a new threading method called FR-t5 (fold recognition by use of 5 terms). In benchmark testings, we have found the consideration of local structural preference potentials in FR-t5 not only greatly enhances the alignment accuracy and recognition sensitivity, but also significantly improves the quality of prediction models.
authors.affiliation: National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Hu
authors.forename: Xiaoxi
authors.initials: X
authors.lastname: Dong
authors.forename: Aiping
authors.initials: A
authors.lastname: Wu
authors.forename: Yang
authors.initials: Y
authors.lastname: Cao
authors.forename: Liqing
authors.initials: L
authors.lastname: Tian
authors.forename: Taijiao
authors.initials: T
authors.lastname: Jiang
mesh_terms: D000595:Amino Acid Sequence / Q000502:physiology; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D008954:Models, Biological; D008958:Models, Molecular; D010363:Pattern Recognition, Automated / Q000379:methods*; D010446:Peptide Fragments / Q000032:analysis / Q000737:chemistry; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein / Q000379:methods
chemical_list: D010446:Peptide Fragments