
LOOPER
 Referenced in 1 article
[sw17376]
 LOOPER: A molecular mechanicsbased 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 MonteCarlo 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 intermolecular interactions.This paper introduces GIBS ... cavitybias algorithm to achieve high sampling acceptance rates for inserting ions and solvent hard ... trivalent (CoHex3+) around fixed allatom models of 25 basepair 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 highlevel language and interactive...

MiniSat
 Referenced in 541 articles
[sw00577]
 An extensible SATsolver. 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, opensource math software...

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