
MAXFLOW
 Referenced in 125 articles
[sw13223]
 /MaxFlow Algorithms for Energy Minimization in Vision.” Yuri Boykov and Vladimir Kolmogorov...

ViennaRNA
 Referenced in 22 articles
[sw10504]
 structures. RNA secondary structure prediction through energy minimization is the most used function ... algorithms for structure prediction: the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields...

SMMP
 Referenced in 12 articles
[sw00882]
 various modern Monte Carlo algorithms and energy minimization routines. The energy of the protein...

CONTRAfold
 Referenced in 8 articles
[sw17117]
 several decades, free energy minimization methods have been the dominant strategy for single sequence ... probabilistic methods have not replaced free energy minimization methods as the tool of choice...

GLOPEQ
 Referenced in 15 articles
[sw07709]
 global minimum of the Gibbs free energy as efficiently as possible, for cases where ... relevance: (i) the minimization of the Gibbs free energy, denoted (G), and (ii) the minimization ... fewer variables than the minimization of the Gibbs free energy. Results for several examples...

NAMD2
 Referenced in 21 articles
[sw09642]
 algorithms to ensure that energy drifts are minimized, ensuring accuracy in long running calculations...

DeepFlow
 Referenced in 9 articles
[sw31217]
 valuable asset for integration into an energy minimization framework for optical flow estimation. Deep Flow...

CP2K
 Referenced in 8 articles
[sw15391]
 dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using...

UNAFold
 Referenced in 8 articles
[sw12671]
 stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling...

EpicFlow
 Referenced in 5 articles
[sw31215]
 sparse set of matches; ii) variational energy minimization initialized with the dense matches. The sparse ... interpolation step, standard onelevel variational energy minimization is carried out on the dense matches...

FROSch
 Referenced in 7 articles
[sw32201]
 ShyLUpackage. The preconditioner uses an energyminimizing coarse space and can be constructed from...

GRIP
 Referenced in 10 articles
[sw12696]
 forcedirected method together with fast energy function minimization. The algorithm underlying the system employs...

Attribute2Image
 Referenced in 4 articles
[sw24589]
 latent representations. We use a general energy minimization algorithm for posterior inference of latent variables...

HotKnots
 Referenced in 4 articles
[sw17267]
 alternative secondary structures, using a free energy minimization algorithm for pseudoknot free secondary structures...

GEMS3K
 Referenced in 4 articles
[sw19058]
 solid solutions, and melts). Direct Gibbs energy minimization (GEM) methods have numerous advantages...

GSGPEs
 Referenced in 9 articles
[sw10779]
 into Hermite functions and direct minimization of the energy functional through a Newtonlike method...

BOSS
 Referenced in 3 articles
[sw27537]
 calculations. The MM calculations cover energy minimizations, normal mode analysis, and conformational searching with ... computing properties of a pure liquid, free energies of solvation, effects of solvation on relative...

TINKER
 Referenced in 10 articles
[sw04095]
 with derivatives, simple free energy perturbation facility, normal mode analysis, minimization in Cartesian, torsional ... dynamics, pairwise neighbor lists and splined spherical energy cutoff methods, particle mesh Ewald (PME) summation ... methods for global optimization, Monte Carlo Minimization (MCM) for efficient potential surface scanning, and more...

fREEDA
 Referenced in 2 articles
[sw07476]
 concepts supporting multi physics modeling. It minimizes energy rather than minimizing current errors...

CHARMMGUI
 Referenced in 2 articles
[sw21732]
 CHARMM performs standard molecular dynamics and energy minimization with the potential energy functions for proteins...