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  • DYANA
  • Referenced in 11 articles [sw08628]
  • conformation space in torsion angle dynamics calculations. Torsion angle dynamics (TAD) performs molecular dynamics simulation ... application of TAD, unbiased sampling of conformation space is essential.par This paper presents a systematic...

  • Cormorant
  • Referenced in 2 articles [sw42205]
  • space. Cormorant significantly outperforms competing algorithms in learning molecular Potential Energy Surfaces from conformational geometries...

  • ZIBMolPy
  • Referenced in 1 article [sw10716]
  • conformational space of molecules. ZIBMolPy couples ZIBgridfree to the state-of-the-art molecular dynamics...

  • CAVER
  • Referenced in 1 article [sw20702]
  • transport pathway often leads through void spaces in the structure. The properties of transport pathways ... therefore, the analysis of a trajectory from molecular dynamics rather than of a single static ... large amount of conformations needed to properly describe conformational space of protein structure. In this ... potential pathways in each snapshot of a molecular dynamics trajectory and clustering is then used...

  • AXIOM
  • Referenced in 173 articles [sw00063]
  • Axiom is a general purpose Computer Algebra system...

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

  • Cuba
  • Referenced in 77 articles [sw00173]
  • Cuba -- a library for multidimensional numerical integration. The...

  • GAP
  • Referenced in 3189 articles [sw00320]
  • GAP is a system for computational discrete algebra...

  • Gmsh
  • Referenced in 767 articles [sw00366]
  • Gmsh is a 3D finite element grid generator...

  • HSL
  • Referenced in 279 articles [sw00418]
  • HSL (formerly the Harwell Subroutine Library) is a...

  • hypre
  • Referenced in 329 articles [sw00426]
  • hypre is a software library for the solution...

  • LAPACK
  • Referenced in 1702 articles [sw00503]
  • LAPACK is written in Fortran 90 and provides...

  • LGO
  • Referenced in 96 articles [sw00516]
  • The program system LGO serves to solve global...

  • LSQR
  • Referenced in 394 articles [sw00530]
  • Algorithm 583: LSQR: Sparse Linear Equations and Least...

  • Macaulay2
  • Referenced in 1923 articles [sw00537]
  • Macaulay2 is a software system devoted to supporting...

  • Magma
  • Referenced in 3315 articles [sw00540]
  • Computer algebra system (CAS). Magma is a large...

  • Maple
  • Referenced in 5373 articles [sw00545]
  • The result of over 30 years of cutting...

  • Mathematica
  • Referenced in 6355 articles [sw00554]
  • Almost any workflow involves computing results, and that...

  • Matlab
  • Referenced in 13544 articles [sw00558]
  • MATLAB® is a high-level language and interactive...