Assembly of low-energy protein conformations with heterogeneous fragments

Author

Molloy, Kevin ; Shehu, Amarda

Author_Institution

Dept. of Comput. Sci., George Mason Univ., Fairfax, VA, USA

fYear

2011

fDate

12-15 Nov. 2011

Firstpage

991

Lastpage

993

Abstract

The most successful ab-initio protein structure prediction methods employ fragment-based assembly. This technique is usually implemented in the context of a Metropolis Monte Carlo template. Fragment length is an important consideration, as it controls the complexity of the discretization of the search space and the associated energy surface. This work measures the impact of employing multiple, heterogeneous fragment lengths in the context of a multi-stage probabilistic search framework.

Keywords

Monte Carlo methods; ab initio calculations; biology computing; molecular biophysics; molecular configurations; proteins; ab initio protein structure prediction method; energy surface; fragment based assembly; fragment length; heterogeneous fragments; low energy protein conformation; metropolis Monte Carlo template; multistage probabilistic search framework; search space; Assembly; Complexity theory; Libraries; Probabilistic logic; Protein engineering; Proteins; Trajectory; fragment-based assembly; near-native conformations; protein native structure;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics and Biomedicine Workshops (BIBMW), 2011 IEEE International Conference on

Conference_Location

Atlanta, GA

Print_ISBN

978-1-4577-1612-6

Type

conf

DOI

10.1109/BIBMW.2011.6112533

Filename

6112533