DocumentCode :
81647
Title :
Ligand-K 
Sequence Elimination: A Novel Algorithm for Ensemble-Based Redesign of Receptor-Ligand Binding
Author :
Qingliang Shen ; Hong Tian ; Daoqi Tang ; Wenbing Yao ; Xiangdong Gao
Author_Institution :
Coll. of Life Sci. & Technol., China Pharm. Univ., Nanjing, China
Volume :
11
Issue :
3
fYear :
2014
fDate :
May-June 2014
Firstpage :
573
Lastpage :
578
Abstract :
K* is rotamerically ensemble-based approach to compute the binding constant. However, its time-consuming feature limited its application. We present a novel algorithm that not only computes the partition function efficiently, but also avoids the exponential growth of execution time by iteratively pruning the sequence space until the sequence with highest affinity is identified.
Keywords :
bioinformatics; bonds (chemical); design; iterative methods; molecular biophysics; rotational isomerism; sequences; binding constant computation; ensemble-based redesign algorithm; execution time exponential growth; iterative sequence space pruning; ligand-K sequence elimination; partition function computation algorithm; receptor-ligand binding; rotameric ensemble-based approach; sequence affinity; Algorithm design and analysis; Bioinformatics; Computational biology; Partitioning algorithms; Pharmaceuticals; Proteins; Ensemble; K* algorithm; protein redesign; sequence elimination;
fLanguage :
English
Journal_Title :
Computational Biology and Bioinformatics, IEEE/ACM Transactions on
Publisher :
ieee
ISSN :
1545-5963
Type :
jour
DOI :
10.1109/TCBB.2014.2302795
Filename :
6728628
Link To Document :
