title: Protein short loop prediction in terms of a structural alphabet.
abstract: Loops connect regular secondary structures. In many instances, they are known to play crucial biological roles. To bypass the limitation of secondary structure description, we previously defined a structural alphabet composed of 16 structural prototypes, called Protein Blocks (PBs). It leads to an accurate description of every region of 3D protein backbones and has been used in local structure prediction. In the present study, we used our structural alphabet to predict the loops connecting two repetitive structures. Thus, we showed interest to take into account the flanking regions, leading to prediction rate improvement up to 19.8%, but we also underline the sensitivity of such an approach. This research can be used to propose different structures for the loops and to probe and sample their flexibility. It is a useful tool for ab initio loop prediction and leads to insights into flexible docking approach.
authors.affiliation: Laboratoire de Biochimie et Génétique Moléculaire, Université de La Réunion, BP 7151, 15 avenue René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France.
authors.forename: Manoj
authors.initials: M
authors.lastname: Tyagi
authors.forename: Aurélie
authors.initials: A
authors.lastname: Bornot
authors.forename: Bernard
authors.initials: B
authors.lastname: Offmann
authors.forename: Alexandre G
authors.initials: AG
authors.lastname: de Brevern
mesh_terms: D003198:Computer Simulation; D030562:Databases, Protein; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D011506:Proteins