• 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...
  • FIDAP

  • Referenced in 37 articles [sw00006]
  • FIDAP (A Fluid Dynamics Analysis Program). This paper...
  • ANSYS

  • Referenced in 704 articles [sw00044]
  • ANSYS offers a comprehensive software suite that spans...
  • BoomerAMG

  • Referenced in 196 articles [sw00086]
  • BoomerAMG: A parallel algebraic multigrid solver and preconditioner...
  • CGAL

  • Referenced in 394 articles [sw00118]
  • The goal of the CGAL Open Source Project...
  • CSDP

  • Referenced in 202 articles [sw00169]
  • CSDP, A C Library for Semidefinite Programming. This...