Biomedical Engineering Reference
In-Depth Information
Table 12.2
RNA secondary structure viewers/editors programs
Name
URL
Description
PseudoViewer (Han et al.
1999
; Byun and Han
2009
)
visualize RNA pseudoknot 2D
structure automatically
RNAdraw (Matzura and
Wennborg
1996
)
RNA 2D structure prediction,
analysis, and visualization
RNA Movies (Evers and
Giegerich
1999
)
System for the visualization of RNA
secondary structure spaces
RNAView/RnamlView
(Yang et al.
2003
)
Automatically generate 2D displays
of RNA/DNA secondary
structures with tertiary
interactions
VARNA (Darty et al.
2009
)
Automated drawing, visualization,
and annotation of the secondary
structure of RNA
RNA Designer
(Andronescu et al.
2004
)
Design de novo RNA structures with
certain structural properties
RnaViz 2
(De Rijk et al.
2003
)
Drawings of RNA secondary
structure with portability and
structure annotation
Vienna RNA (Hofacker
2003
)
Program for the prediction and
comparison of RNA secondary
structures
In spite of these advantages, RNA has not been focus of structure-based drug
design, not only due to lack of information of RNA 3D structures, but also due to the
sequence-specific unique features of the binding pockets in RNA. The binding pocket
of protein usually lies deep in an internal region, separated from solvent. In RNA
targets, the binding pockets are large and flat, located along the surface, and rela-
tively exposed to solvent. Therefore, in using docking algorithms to discover RNA-
binding drugs, the physicochemical properties of RNA, such as conformational
flexibility, high negative charge, and solvation, should be taken into account more
accurately than those for proteins. Despite such differences between protein and
RNA targets, classical protein-ligand docking programs have sometimes success-
fully performed in RNA-targeted virtual screenings. For example, Kuntz first reported
a successful virtual screening using DOCK 3.5 program to identify small molecules
in the Available Chemicals Directory (ACD) that targeted an RNA double helix
(Chen et al.
1997
). Following the first study, many research groups have reported
successful studies of virtual screening targeting RNA through protein-based docking
methods (Filikov et al.
2000
; Lind et al.
2002
; Kang et al.
2004
; Park et al.
2008,
2011
). Meanwhile, since most of the available docking methods were developed for
protein targets, their compliance with RNA targets has been evaluated extensively,
and recently Li et al. demonstrated that two widely-used protein docking programs,
GOLD 4.0 and Glide 5.0, are appropriate for structure-based drug design and virtual
screening for RNA targets (Detering and Varani
2004
; Li et al.
2010
) .
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