ARCIMBOLDO_LITE: single-workstation implementation and use

Acta Crystallogr D Biol Crystallogr. 2015 Sep;71(Pt 9):1921-30. doi: 10.1107/S1399004715010846. Epub 2015 Aug 25.

Abstract

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.

Keywords: ARCIMBOLDO_BORGES; ab initio; phasing; small fragments.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Computers*
  • Database Management Systems*
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Proteins / chemistry*
  • Software

Substances

  • Proteins