Bioinformatics Links Directory : Structure Prediction, Visualization, and DesignContains links to applications for the visualization, prediction, and design of RNA molecules including siRNAs, secondary structure, and folding kinetics.Mfold- (Found July 2, 2008 ) Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS.http://www.bioinfo.rpi.edu/applications/mfold/old/rna/ MolMovDB- (Found July 2, 2008 ) The Database of Macromolecular Movements (MolMovDB) contains a collection of animated protein and RNA structures to assist in the exploration of macromolecular flexibility. Software for structure analysis is also available.http://molmovdb.org/ MOLPROBITY- (Found July 2, 2008 ) MOLPROBITY is a structure validation program that can calculate and display steric, H-bonding, and van der Waals interactions for 3D structures of proteins, nucleic acids, and complexes.http://molprobity.biochem.duke.edu/ Pfold- (Found July 2, 2008 ) The Pfold server takes an alignment of RNA sequences as input and predicts a common secondary structure.http://www.daimi.au.dk/~compbio/pfold PKNOTS- (Found July 2, 2008 ) Predict pseudoknot structures in RNA sequence; source code only.http://www.genetics.wustl.edu/eddy/software/#pk Vienna RNA Package- (Found July 2, 2008 ) Comprises a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.http://www.tbi.univie.ac.at/~ivo/RNA/ |