Skip to Main content Skip to Navigation
Journal articles

Protein short loop prediction in terms of a structural alphabet.: protein short loops prediction

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.
Complete list of metadatas

https://www.hal.inserm.fr/inserm-00396485
Contributor : Alexandre G. de Brevern <>
Submitted on : Tuesday, August 4, 2009 - 11:22:18 AM
Last modification on : Tuesday, November 3, 2020 - 11:18:02 AM
Long-term archiving on: : Tuesday, June 15, 2010 - 5:35:37 PM

Identifiers

Citation

Manoj Tyagi, Aurélie Bornot, Bernard Offmann, Alexandre de Brevern. Protein short loop prediction in terms of a structural alphabet.: protein short loops prediction. Computational Biology and Chemistry, Elsevier, 2009, 33 (4), pp.329-33. ⟨10.1016/j.compbiolchem.2009.06.002⟩. ⟨inserm-00396485⟩

Share

Metrics

Record views

533

Files downloads

1397