MFOLD
MFOLD is a widely used nucleic acid secondary structure prediction program
developed by Dr.
Michael Zuker using thermodynamic methods. Dr. Zuker provides the
web interface for both RNA-folding
and DNA-folding.
The source
codes and executables can be downloaded.
Hybrid
Hybrid
is a a program developed by Dr. Zuker to calculate the hybridization of
two different stands of DNA or RNA. The source
codes and executables can be downloaded.
RNABase
RNABase is a database
for RNA Structure.
NDB
The Nucleic Acid
Database Project (NDB) is a repository of three-dimensional structural
information about nucleic acids
SCOR
Structural Classification
of RNA Database (SCOR) is a database designed to provide a comprehensive
perspective and understanding of RNA motif structure, function, tertiary
interactions and their relationships.
World Index of Molecular Visualization Resources
World
Index of Molecular Visualization Resources is a repository of links
to tutorials, demos, structural databases, galleries of images and visualization
programs.
Mc-Sym
Mc-Sym
is a software program that builds RNA 3-D structures using coordinates
and relations between residues extracted from X-ray crystallography
and NMR found in the RCSB Protein Data Bank and the Rutgers Nucleic
Acid Database and from theoretical models.
Vienna RNA Package
Vienna
RNA Package is a programming package to predict RNA secondary structure
through energy minimization.
COVE, RNABOB, and PKNOTs
COVE,
RNABOB,
and PKNOTs
are programs developed by Dr. Sean Eddy. COVE
is for RNA structure analysis using covariance models; RNABOB
is for pattern searching for RNA secondary structures; and PKNOTs
is for RNA pseudoknot prediction.
RNAdraw
RNAdraw is an integrated
program for RNA secondary structure calculation and analysis.
SStructView
SStructView
is a Java applet for RNA secondary structure.
