Designability of lattice small-size protein models: is it sufficient to use the compact ground states?

Traditionally, only the maximally compact ground states are considered in the designability studies of the lattice proteins. We consider the consequences of inclusion of all clustered conformations as an extended set of the ground states. We calculated designabilities and performed folding simulatio...

Full description

Saved in:
Bibliographic Details
Published in:Chemical physics letters 2004-04, Vol.388 (4), p.348-352
Main Authors: Yesylevskyy, S.O, Demchenko, A.P
Format: Article
Language:English
Citations: Items that this one cites
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Traditionally, only the maximally compact ground states are considered in the designability studies of the lattice proteins. We consider the consequences of inclusion of all clustered conformations as an extended set of the ground states. We calculated designabilities and performed folding simulations for 12-mers using traditional and extended ground state definitions. We show that the choice of compact conformations as the ground states may produce severe artifacts in designability and folding kinetics studies, even for such small model systems. The physically realistic concept of the clustered ground states allows to overcome these difficulties.
ISSN:0009-2614
1873-4448
DOI:10.1016/j.cplett.2004.03.021