ARCIMBOLDO_LITE: single‐workstation implementation and use. (1st September 2015)

• Record Type: Journal Article
• Authors: Sammito, Massimo; Millán, Claudia; Frieske, Dawid; Rodríguez‐Freire, Eloy; Borges, Rafael J.; Usón, Isabel
• Is Part Of: Acta crystallographica. Volume 71:Part 9(2015:Sep.)
• Page Start: 1921
• Page End: 1930
• Publication Date: 2015-09-01
• Subjects: Biomolecules -- Structure -- Periodicals; Physical biochemistry -- Periodicals; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; 572
• DOI: 10.1107/S1399004715010846
• Languages: English
• ISSNs: 0907-4449

Abstract

<abstract abstract-type="main" xml:lang="en"> <title> <x xml:space="preserve">Abstract</x> </title> <p> <italic>ARCIMBOLDO</italic> 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, <italic>ARCIMBOLDO_LITE</italic>, 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. <italic>ARCIMBOLDO_BORGES</italic> 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. <italic>ARCIMBOLDO</italic> has been thoroughly rewritten and three binaries are now available: <italic>ARCIMBOLDO_LITE</italic>, <italic>ARCIMBOLDO_SHREDDER</italic> and <italic>ARCIMBOLDO_BORGES</italic>. The programs and libraries can be downloaded from <ext-link ext-link-type="uri" xlink:href="http://chango.ibmb.csic.es/ARCIMBOLDO_LITE" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">http://chango.ibmb.csic.es/ARCIMBOLDO_LITE</ext-link>.</p> </abstract>