PMID- 22183536
OWN - NLM
STAT- MEDLINE
DCOM- 20120413
LR  - 20111220
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 819
DP  - 2012
TI  - Normal mode-based approaches in receptor ensemble docking.
PG  - 157-68
LID - 10.1007/978-1-61779-465-0_11 [doi]
AB  - Explicitly accounting for target flexibility in docking still constitutes a 
      difficult challenge due to the high dimensionality of the conformational space to 
      be sampled. This especially applies to the high-throughput scenario, where the 
      screening of hundreds of thousands compounds takes place. The use of multiple 
      receptor conformations (MRCs) to perform ensemble docking in a sequential fashion 
      is a simple but powerful approach that allows to incorporate binding site 
      structural diversity in the docking process. Whenever enough experimental 
      structures to build a diverse ensemble are not available, normal mode analysis 
      provides an appealing and efficient approach to in silico generate MRCs by 
      distortion along few low-frequency modes that represent collective mid- and 
      large-scale displacements. In this way, the dimension of the conformational space 
      to be sampled is heavily reduced. This methodology is especially suited to 
      incorporate target flexibility at the backbone level. In this chapter, the main 
      components of normal mode-based approaches in the context of ensemble docking are 
      presented and explained, including the theoretical and practical considerations 
      needed for the successful development and implementation of this methodology.
FAU - Cavasotto, Claudio N
AU  - Cavasotto CN
AD  - School of Biomedical Informatics, The University of Texas Health Center, Houston, 
      TX, USA. claudio.n.cavasotto@uth.tmc.edu
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
RN  - 0 (Receptors, Cell Surface)
SB  - IM
MH  - *Algorithms
MH  - Computational Biology/*methods
MH  - Protein Binding
MH  - Protein Conformation
MH  - Receptors, Cell Surface/*chemistry
EDAT- 2011/12/21 06:00
MHDA- 2012/04/14 06:00
CRDT- 2011/12/21 06:00
PHST- 2011/12/21 06:00 [entrez]
PHST- 2011/12/21 06:00 [pubmed]
PHST- 2012/04/14 06:00 [medline]
AID - 10.1007/978-1-61779-465-0_11 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2012;819:157-68. doi: 10.1007/978-1-61779-465-0_11.