Geometric algorithms for the conformational analysis of long protein loops - Archive ouverte HAL Access content directly
Journal Articles Journal of Computational Chemistry Year : 2004

Geometric algorithms for the conformational analysis of long protein loops

(1) , (1) , (2) , (3)
1
2
3

Abstract

The efficient filtering of unfeasible conformations would considerably benefit the exploration of the conformational space when searching for minimum energy structures or during molecular simulation. The most important conditions for filtering are the maintenance of molecular chain integrity and the avoidance of steric clashes. These conditions can be seen as geometric constraints on a molecular model. In this article, we discuss how techniques issued from recent research in robotics can be applied to this filtering. Two complementary techniques are presented: one for conformational sampling and another for computing conformational changes satisfying such geometric constraints. The main interest of the proposed techniques is their application to the structural analysis of long protein loops. First experimental results demonstrate the efficacy of the approach for studying the mobility of loop 7 in amylosucrase from Neisseria polysaccharea. The supposed motions of this 17-residue loop would play an important role in the activity of this enzyme.
Fichier principal
Vignette du fichier
04jcompchem_sub.pdf (308.45 Ko) Télécharger le fichier
Origin : Files produced by the author(s)
Loading...

Dates and versions

hal-01987902 , version 1 (21-01-2019)

Identifiers

Cite

Juan Cortés, Thierry Simeon, Magali Remaud Simeon, V. Tran. Geometric algorithms for the conformational analysis of long protein loops. Journal of Computational Chemistry, 2004, 25 (7), pp.956-967. ⟨10.1002/jcc.20021⟩. ⟨hal-01987902⟩
47 View
0 Download

Altmetric

Share

Gmail Facebook Twitter LinkedIn More