Nussinov  Crack + Full Product Key [Win/Mac] 2022
Given a set of residues within a given RNA-structure, it computes the Nussinov score of these residues.
In case of disordered RNAs, a penalty for ordered regions has been added.
By default, Nussinov calculates the Nussinov score at the base of the stem.
To calculate the Nussinov score at an arbitrary position within the stem, pass in a position parameter to the calculate method.
Example-usage:
// 0 = if == [true] otherwise.
// 1 = un-flipped base, 2 = flipped base.
public double getNussinov(double[] sequence, int position) {
    return calculate(sequence, position, NussinovParams.DOUBLE_UNFLIPPED_0, NussinovParams.DOUBLE_UNFLIPPED_1, NussinovParams.DOUBLE_UNFLIPPED_2);
}
"The Nussinov scores correspond to the stacking energies of the native base-pairs of the native A-minor, in their equilibrium structure."
Parameters:
Parameter          | Description
Nussinov  Crack
Nussinov considers a local 2D conformational space.  It assumes that in a Nussinov calculation, only a single molecule can be in a given conformation.  In this case, Nussinov can be used to calculate the free energy difference between the shortest path to a structure and the structures that constitute the optimum of that conformational space.  It is advantageous for use in situations where the input structure ensemble is significantly larger than the space in which the algorithms are parameterised.
Nussinov calculates energies at the lowest energy structure of the input ensemble and builds local optima graphs that are biased towards the lowest energy structure.  It then finds the lowest energy structure that is not in the input ensemble and an estimate of the lowest energy structure which is a possible outlier.  This last step is repeated, starting from the highest probability conformation in the input ensemble and performing a move to a conformation that is approximately equally probable until a structure is found to be an outlier.  The final free energy estimate is calculated.
Nussinov and its Nussinov Structure Calculator worksheets were developed at the École Polytechnique Fédérale de Lausanne  and are compatible with well known molecular simulation packages, such as CHARMM, AMBER, NAMD and AmberTools.
 
 In 2001, Nussinov was the winner of the Branco Weiss Prize for the best software in computational chemistry.
 Nussinov was the subject of the Science article "A New Algorithm to Calculate the Nussinov Energy".
 In 2004, Nussinov was the subject of the journal Nature article "Computational RNA folding".
 In 2006, Nussinov was the subject of the journal RNA Chemistry article "Simulation of the RNA Folding Dynamics."
 In 2007, Nussinov was the subject of the Journal of Biomolecular NMR article "Nussinov: a new method of parallel computing for RNA molecular dynamics (MD) simulations."
 In 2010, Nussinov was the subject of the Journal of Computational Chemistry article "Computational Calculations of the Energies of Single-Stranded RNA Molecules."
 In 2012, Nussinov and its Nussinov Structure Calculator were used in the study of another winning program—AmberTools for RNA.  The study led to the use of Nussinov as a first line tool to predict structures
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