Mathematical software

ViennaRNA
Referenced in 23 articles [sw10504]
secondary structures. RNA secondary structure prediction through energy minimization is the most used function ... programming algorithms for structure prediction: the minimum free energy algorithm of (Zuker & Stiegler 1981) which...

GLOPEQ
Referenced in 15 articles [sw07709]
total Gibbs free energy of the system be at its global minimum ... corresponding to a global minimum of the Gibbs free energy as efficiently as possible...

RNAfold
Referenced in 5 articles [sw10505]
RNAfold 2.1.8: Calculate minimum free energy secondary structures and partition function of RNAs. The program ... sequences from stdin, calculates their minimum free energy (mfe) structure and prints to stdout...

RNAsubopt
Referenced in 6 articles [sw10506]
user defined energy range above the minimum free energy (mfe). It prints the suboptimal structures...

MiPred
Referenced in 5 articles [sw29580]
local contiguous structure-sequence composition, minimum of free energy (MFE) of the secondary structure...

RNAexinv
Referenced in 2 articles [sw17114]
also the mutational robustness and the minimum free energy. The sequences that are generated...

TIRNA
Referenced in 2 articles [sw36916]
between two RNA molecules based on minimum free energy (MFE). The algorithm is stand...

GtRNAdb
Referenced in 2 articles [sw23001]
structural impacts from sequence variants and minimum free energy structural predictions. Views of tRNA genes...

KnotSeeker
Referenced in 1 article [sw36931]
Practical structure prediction algorithms based on free energy minimization employ a restricted problem class ... optimal solution in regards to the minimum free energy model. We present KnotSeeker ... uses a hybrid sequence matching and free energy minimization approach to perform a screening ... existing dynamic programming algorithm and a minimum weight independent set calculation. KnotSeeker is significantly more...

ERD
Referenced in 1 article [sw23801]
target RNA secondary structure, i.e. whose minimum free energy (MFE) structure is the target structure...

RNASurface
Referenced in 1 article [sw23120]
efficiently constructing a matrix of RNA minimum free energies. A wide range of lengths...

ShengBTE
Referenced in 3 articles [sw17641]
Dirac delta distributions arising from conservation of energy are approximated by Gaussian functions. A locally ... renders the method fully parameter free. The code is free software, written in Fortran ... third-order interatomic force constants from a minimum number of ab-initio calculations, using...

LS-VISM
Referenced in 3 articles [sw16158]
method for relaxing the VISM free-energy functional and a compact coupling interface method ... simple and flexible with respect to minimum adjustable parameters and a wide range of applications...

RandSpg
Referenced in 1 article [sw25040]
generated, and factors that influence the minimum interatomic separations. In addition, the user can optionally ... reliable. The library is lightweight, portable, dependency-free and is published under a license recognized ... optimized to find the global energy minimum...

MinimumEnergyPoints
Referenced in 2 articles [sw34576]
spheres and their application in mesh-free interpolation and differentiation. It is known that discrete ... obtained from minimizing the energy functional corresponding to Riesz (s)-kernels (k_s(oldsymbol ... kernels for both the generation of the minimum energy points and the spherical basis functions...

ViennaRNA