The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently o#ers prediction of secondary structure from a single sequence, prediction of the consensus

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Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions

structure

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ABSTRACT We have developed an auto-matic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone tor-sional angle information. Parameters of the pattern recognition procedure were

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We present a new method for predicting the secondary structure of globular proteins based on non-linear neural network models. Network models learn from existing protein structures how to predict the secondary structure of local sequences of amino acids. The average success rate of our method on a

An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm is particularly fast in the vicinity of the minimum free energy. This enables the efficient approximation of statistical quantities

Secondary structures of polynucleotides can be view as a certain class of planar vertex-labeled graphs. We construct recursion formulae enumerating various sub-classes of these graphs as well as certain structural elements (sub-graphs). First order asymptotics are derived and their dependence