Nussinov was created as an easy-to-use, simple and dynamic programming algorithm for the calculation of the Nussinov of 2D structures of RNA.
Nussinov is written using Java and is available for all major platforms, including Windows, Mac OS X and Linux.
Nussinov
This algorithm has been implemented in the Nussinov: A dynamic programming algorithm for the calculation of the Nussinov.
Input:
a DNA string
an integer K = 0 (default K = 10)
Output:
the Nussinov of this DNA string
See also
Capra
References
Further reading
External links
nussinov – Nussinov – RNA secondary structure prediction by K.G.Bruno, H.W.Klein and J.D.Nielsen .
nussinov – Nussinov – RNA secondary structure prediction by K.G.Bruno and H.W.Klein.
Category:Bioinformatics
Category:RNA
Category:Bioinformatics software
Category:StructureQ:
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Nussinov Crack + Activation Key
Nussinov Crack Mac 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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Nussinov Crack + Keygen
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
What’s New in the Nussinov?
Example usage:
An example Nussinov calculation is as follows, where the cost of moving between states is ignored. In this example, the state is ignored where both sides have the same number of base pairs (e.g., the states AB and AB are equal).
public static final int[][] Nussinov(int nbSections, int[][] states) {
// Input:
// 1) Number of sections
// 2) List of states
//
// Output:
// 1) Minimum Nussinov total cost of state path
// 2) State path with lowest cost
//
// This returns an array containing the costs of a state path, where the states are represented as an array of arrays of section costs. The last row of the matrix is initialized to the cost of a state of nbSections (number of sections) where all states have the same cost (e.g., the state NUCLEOTIDE GUG-3D-GGU with cost 4 + 3 = 7), which is assumed to be 1.
//
// States:
//
//
//
//
// The following states are not used, but aren’t included in the calculation:
//
//
//
// The Nussinov cost is the sum of the costs of all states along a path, calculated as follows.
//
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System Requirements For Nussinov:
Minimum:
OS: Windows 7 (32-bit and 64-bit)
Processor: Intel Core i3, Intel Core i5, or AMD Phenom II X3
Memory: 2 GB RAM
Graphics: Intel HD 4000, NVidia 650, or ATI Radeon HD 4870
DirectX: Version 9.0c
Network: Broadband Internet connection
Storage: 4 GB available space
Sound Card: DirectX 9.0c Compatible sound card or onboard sound
Additional Notes:
Running version 1607
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