• ERATO

  • Referenced in 39 articles [sw11922]
  • equilibrium, the evolution of the normal modes can be calculated by linearizing the ideal...
  • GENESIS

  • Referenced in 13 articles [sw02283]
  • finite element method for static, normal modes, direct and modal frequency analysis, random response analysis...
  • CASTOR

  • Referenced in 8 articles [sw09186]
  • CASTOR: normal-mode analysis of resistive MHD plasmas. The CASTOR (complex Alfvén spectrum of toroidal ... code computes the entire spectrum of normal modes in resistive MHD for general tokamak configurations...
  • TINKER

  • Referenced in 10 articles [sw04095]
  • derivatives, simple free energy perturbation facility, normal mode analysis, minimization in Cartesian, torsional or rigid...
  • TAF

  • Referenced in 81 articles [sw07492]
  • programs. TAF supports forward and reverse mode of AD and Automatic Sparsity Detection ... sparsity structure of Jacobians. TAF normalizes the code and applies a control flow analysis...
  • Qn3d

  • Referenced in 5 articles [sw18099]
  • adequately explained the behavior of this mode. A particle-in-cell (PIC) model in Cartesian ... particle motion is analyzed. Next the normal modes are calculated and simulated. Finally, QN3D...
  • Teukode

  • Referenced in 5 articles [sw11318]
  • very prolonged, weakly damped, quasi-normal-mode phase. For extremal rotation, the field at future...
  • Bio3d

  • Referenced in 3 articles [sw15706]
  • analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure ... data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various...
  • MacMolPlt

  • Referenced in 3 articles [sw07039]
  • data read in you can animation normal modes, or geometry optimizations ... molecule display and various normal mode display options are controlled via the Display menu. Atomic...
  • iMod

  • Referenced in 4 articles [sw35118]
  • iMod: multipurpose normal mode analysis in internal coordinates. Results: Here, we present a new versatile...
  • ENCoM

  • Referenced in 2 articles [sw16880]
  • stability. ENCoM is a coarse-grained normal mode analysis method recently introduced that unlike previous ... first time a coarse-grained normal mode analysis method to predict the effect of single...
  • ElNemo

  • Referenced in 1 article [sw22480]
  • ElNemo: a normal mode web server for protein movement analysis and the generation of templates ... molecular replacement. Normal mode analysis (NMA) is a powerful tool for predicting the possible movements ... using at most two low-frequency normal modes. Applications of NMA cover wide areas ... determination by X-ray crystallography, where normal mode perturbed models are used as templates...
  • GANM

  • Referenced in 1 article [sw08551]
  • approach based on genetic algorithm and normal modes. We describe a new method ... software, called GANM (Genetic Algorithm with Normal Modes), that combines genetic algorithm and normal mode ... binding site. The methodology uses normal modes to account for the global conformational changes...
  • DISPER80

  • Referenced in 2 articles [sw16467]
  • package for the calculation of seismic normal-mode solutions...
  • MOIL

  • Referenced in 2 articles [sw35737]
  • applications such as energy, energy minimization, normal modes, dynamics and free energy calculations code...
  • BOSS

  • Referenced in 2 articles [sw27537]
  • calculations cover energy minimizations, normal mode analysis, and conformational searching with the OPLS force fields...
  • NRGTEN

  • Referenced in 1 article [sw36446]
  • extensible toolkit for coarse-grained normal mode analysis of proteins, nucleic acids, small molecules ... their complexes. Coarse-grained normal mode analysis (NMA) is a fast computational technique to study...
  • KrakanC

  • Referenced in 1 article [sw07442]
  • method is proposed for finding the normal mode eigenvalues in shallow water waveguide. We transform ... well with that calculated by the normal mode program KrakanC...
  • RedMD

  • Referenced in 1 article [sw32713]
  • perform molecular dynamics simulations and normal mode analysis of reduced models of proteins, nucleic acids ... potential energy functions. Normal mode analysis tool is available for elastic or anisotropic network models...
  • Mineos

  • Referenced in 1 article [sw32441]
  • symmetric non-rotating Earth by summing normal modes. Attenuation, gravity and transversal anisotropy effects...