By Topic

Potential function of simplified protein models for discriminating native proteins from decoys: combining contact interaction and local sequence-dependent geometry

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$31 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

3 Author(s)
Zhang, J. ; Dept. of Bioeng., Illinois Univ., Chicago, IL, USA ; Chen, R. ; Liang, Jie

An effective potential function is critical for protein structure prediction and folding simulation. For simplified models of proteins where coordinates of only Ca atoms need to be specified, an accurate potential function is important. Such a simplified model is essential for efficient search of conformational space. In this work, we present a formulation of potential function for simplified representations of protein structures. It is based on the combination of descriptors derived from residue-residue contact and sequence-dependent local geometry. The optimal weight coefficients for contact and local geometry is obtained through optimization by maximizing margins among native and decoy structures. The latter are generated by chain growth and by gapless threading. The performance of the potential function in blind test of discriminating native protein structures from decoys is evaluated using several benchmark decoy sets. This potential function have comparable or better performance than several residue-based potential functions that require in addition coordinates of side chain centers or coordinates of all side chain atoms.

Published in:

Engineering in Medicine and Biology Society, 2004. IEMBS '04. 26th Annual International Conference of the IEEE  (Volume:2 )

Date of Conference:

1-5 Sept. 2004