• 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...