• LOOPER

  • Referenced in 1 article [sw17376]
  • LOOPER: A molecular mechanics-based algorithm for protein loop prediction. We describe ... LOOPER, for the prediction of protein loop conformations. The method is based on a multi ... initio computational loop modeling is the exponential growth of the backbone conformational states with ... that use Monte-Carlo schemes or exhaustive sampling, LOOPER adopts a systematic search strategy with...
  • Prodock

  • Referenced in 1 article [sw33075]
  • protein is represented by an all‐atom model with the Ecepp /3 or Amber ... programming easier and the definition of molecular flexibility more straigthforward. Two versions of the dictionary ... local minimization during the conformational sampling has been shown to be very important for distinguishing...
  • GIBS

  • Referenced in 1 article [sw19743]
  • biomolecules strongly influences their structure, conformational stability, and inter-molecular interactions.This paper introduces GIBS ... cavity-bias algorithm to achieve high sampling acceptance rates for inserting ions and solvent hard ... trivalent (CoHex3+) around fixed all-atom models of 25 base-pair nucleic acid duplexes. GIBS...
  • Cuba

  • Referenced in 60 articles [sw00173]
  • Cuba -- a library for multidimensional numerical integration. The...
  • Gmsh

  • Referenced in 627 articles [sw00366]
  • Gmsh is a 3D finite element grid generator...
  • HSL

  • Referenced in 274 articles [sw00418]
  • HSL (formerly the Harwell Subroutine Library) is a...
  • LAPACK

  • Referenced in 1647 articles [sw00503]
  • LAPACK is written in Fortran 90 and provides...
  • LGO

  • Referenced in 93 articles [sw00516]
  • The program system LGO serves to solve global...
  • LSQR

  • Referenced in 368 articles [sw00530]
  • Algorithm 583: LSQR: Sparse Linear Equations and Least...
  • Macaulay2

  • Referenced in 1721 articles [sw00537]
  • Macaulay2 is a software system devoted to supporting...
  • Magma

  • Referenced in 2986 articles [sw00540]
  • Computer algebra system (CAS). Magma is a large...
  • Maple

  • Referenced in 5168 articles [sw00545]
  • The result of over 30 years of cutting...
  • Mathematica

  • Referenced in 6041 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 12477 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • MiniSat

  • Referenced in 541 articles [sw00577]
  • An extensible SAT-solver. MiniSat is a minimalistic...
  • NAG

  • Referenced in 419 articles [sw00610]
  • Produced by experts for use in a variety...
  • R

  • Referenced in 8728 articles [sw00771]
  • R is a language and environment for statistical...
  • SageMath

  • Referenced in 1714 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...
  • SMMP

  • Referenced in 12 articles [sw00882]
  • The SMMP (Simple Molecular Mechanics for Proteins) package...