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ARCIMBOLDO_LITE: single-workstation implementation and use.

Massimo SammitoClaudia MillánDawid FrieskeEloy Rodríguez-FreireRafael J BorgesIsabel Usón
Published in: Acta crystallographica. Section D, Biological crystallography (2015)
ARCIMBOLDO solves the phase problem at resolutions of around 2 Å or better through massive combination of small fragments and density modification. For complex structures, this imposes a need for a powerful grid where calculations can be distributed, but for structures with up to 200 amino acids in the asymmetric unit a single workstation may suffice. The use and performance of the single-workstation implementation, ARCIMBOLDO_LITE, on a pool of test structures with 40-120 amino acids and resolutions between 0.54 and 2.2 Å is described. Inbuilt polyalanine helices and iron cofactors are used as search fragments. ARCIMBOLDO_BORGES can also run on a single workstation to solve structures in this test set using precomputed libraries of local folds. The results of this study have been incorporated into an automated, resolution- and hardware-dependent parameterization. ARCIMBOLDO has been thoroughly rewritten and three binaries are now available: ARCIMBOLDO_LITE, ARCIMBOLDO_SHREDDER and ARCIMBOLDO_BORGES. The programs and libraries can be downloaded from http://chango.ibmb.csic.es/ARCIMBOLDO_LITE.
Keyphrases
  • amino acid
  • high resolution
  • primary care
  • healthcare
  • quality improvement
  • public health
  • single molecule
  • iron deficiency