Biomedical Engineering Reference
In-Depth Information
Table 12.3
Computer program for predicting RNA 3D structure
Name
URL
Short summary
Mode RNA
(Rother et al.
2011
)
Automatic program for comparative
modeling of RNA 3D structures.
Require sequence alignment and
structural template
MMB (formerly
RNA Builder)
(Flores et al.
2010
)
Automatic program for generating model
RNA structures from 2D and template
structure by simulating in parallel at
multiple levels of details
PARADISE (Assemble
and S2S) (Jossinet
et al.
2010
; Jossinet
and Westhof
2005
)
Assemble: automatic program for intuitive
graphical interface to study and
construct complex 3D RNA structures.
S2S: graphical system to easily display,
manipulate, and interconnect heteroge-
neous RNA data like multiple sequence
alignments, 2D and 3D structures
RNA2D3D (Martinez
et al.
2008
)
Manual manipulation program for RNA 3D
modeling with conversion of RNA 2D
structures to 3D
ERNA-3D (Zwieb
and Müller
1997
)
Molecular Modeling Expert System to
develop for the generation of models of
RNA and protein molecules. Need to
manual manipulation
MC-Fold/MC-Sym
(Parisien and Major
2008
)
A web-hosted service for prediction of
RNA 3D structure with input 2D
secondary
NAST (Jonikas et al.
2009
)
Predicting RNA 3D model from 2D
structure
DMD/iFoldRNA
(Sharma et al.
2008
)
Web portal for interactive RNA folding
simulations. Enable to perform
molecular dynamics simulations of
RNA using coarse-grained structural
models (two-beads/residue)
YUP (Tan et al.
2006
)
RNA molecular modeling program based
on PYTHON. Offer such methods as
Monte Carlo, Molecular Mechanics and
Energy Minimization
Several modi fi ed algorithms were established for RNA-targeted virtual screening.
For example, Morley and Afshar established an empirical scoring function that
appropriately describes steric, polar, and charged interactions in RNA-ligand com-
plexes (Morley and Afshar
2004
). This scoring function was implanted in RiboDock
program and validated for docking screening of a large-size chemical database.
Virtual screening with this program successfully identified novel ligands for the
bacterial ribosomal A-site (Foloppe et al.
2004
). Moitessier et al. applied a unique
method to the AutoDock docking process, taking into account inherent RNA
flexibility and key water molecules, and this modified docking tool was validated by
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