• RAPTOR

  • Referenced in 19 articles [sw09002]
  • RAPTOR: optimal protein threading by linear programming. This paper presents a novel linear programming approach ... protein 3D structure template, the protein threading problem is formulated as a large scale integer ... factors in making the protein threading problem NP-hard. A surprising result is that, most ... software package RAPTOR–RApid Protein Threading by Operation Research technique. Large scale benchmark test...
  • I-TASSER

  • Referenced in 18 articles [sw17207]
  • platform for automated protein structure and function prediction. The iterative threading assembly refinement (I-TASSER ... server is an integrated platform for automated protein structure and function prediction based ... multiple threading alignments and iterative structural assembly simulations. The function of the protein is then...
  • VADAR

  • Referenced in 6 articles [sw12496]
  • qualitatively assessing protein structures determined by X-ray crystallography, NMR spectroscopy, 3D-threading or homology...
  • TUNE

  • Referenced in 1 article [sw35757]
  • Threading Using Neural nEtwork (TUNE): the measure of protein sequence - structure compatibility. Motivation: Fold recognition ... programs align a probe protein sequence onto protein three-dimensional (3D) structure templates. The alignment ... Here we present a new threading scoring function of protein sequence–structure compatibility. An artificial...
  • COFACTOR

  • Referenced in 1 article [sw35552]
  • first identifies template proteins of similar folds and functional sites by threading the target structure...
  • 3DCoffee

  • Referenced in 6 articles [sw12008]
  • developed 3DCoffee, a novel method for combining protein sequences and structures in order to generate ... found that combining TCoffee with the threading program Fugue makes it possible to improve...
  • RAPSearch2

  • Referenced in 3 articles [sw23045]
  • achieving similar levels of sensitivity for short protein fragments derived from NGS data. RAPSearch, however ... times. We also implemented multi-threading in RAPSearch2, and the multi-thread modes achieve significant...
  • CUDASW++

  • Referenced in 2 articles [sw17596]
  • bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel ... deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data...
  • MSAProbs

  • Referenced in 3 articles [sw12007]
  • practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based ... multi-core CPUs by employing a multi-threaded design, leading to a competitive execution time...
  • CUDAMPF++

  • Referenced in 1 article [sw21326]
  • variation of query models or protein sequence datasets. For MSV (SSV) kernels, the peak performance ... based implementation (16 cores, 32 threads...
  • Peppy

  • Referenced in 1 article [sw31813]
  • useful method for identifying novel proteins, annotating genes and detecting peptides unique to an individual ... platform execution, the software is fully multi-threaded for enhanced speed. The program...
  • GAP

  • Referenced in 2876 articles [sw00320]
  • GAP is a system for computational discrete algebra...
  • LAPACK

  • Referenced in 1642 articles [sw00503]
  • LAPACK is written in Fortran 90 and provides...
  • Matlab

  • Referenced in 12309 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • NITSOL

  • Referenced in 91 articles [sw00623]
  • We introduce a well-developed Newton iterative (truncated...
  • R

  • Referenced in 8601 articles [sw00771]
  • R is a language and environment for statistical...
  • AMBER

  • Referenced in 54 articles [sw01333]
  • AmberTools is a set of programs for biomolecular...
  • NEURON

  • Referenced in 179 articles [sw03059]
  • Parallel network simulations with NEURON. The NEURON simulation...
  • NAMD

  • Referenced in 77 articles [sw03198]
  • NAMD is a parallel molecular dynamics code designed...