ARCIMBOLDO_LITE: single-workstation implementation and use

Acta Crystallographica. Section D, Biological Crystallography
Massimo SammitoIsabel Usón

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.

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Citations

Sep 4, 2015·Acta Crystallographica. Section D, Biological Crystallography·Claudia MillánIsabel Usón
Jul 1, 2017·Annals of the New York Academy of Sciences·Anja SchuetzUdo Heinemann
Mar 14, 2018·Acta Crystallographica. Section D, Structural Biology·Iracema CaballeroIsabel Usón
Mar 14, 2018·Acta Crystallographica. Section D, Structural Biology·Huw T Jenkins
Apr 14, 2018·Acta Crystallographica. Section D, Structural Biology·Claudia MillánIsabel Usón
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Feb 13, 2018·Nature·Hugo LavoieMarc Therrien
Mar 7, 2020·Acta Crystallographica. Section D, Structural Biology·Claudia MillánIsabel Usón
Mar 7, 2020·Acta Crystallographica. Section D, Structural Biology·Ana MedinaMassimo D Sammito
Aug 4, 2020·Acta Crystallographica. Section D, Structural Biology·Logan S RichardsJose A Rodriguez
Aug 3, 2019·Acta Crystallographica. Section D, Structural Biology·Petra HavlickovaIvana Kuta Smatanova
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Jan 7, 2021·Acta Crystallographica. Section D, Structural Biology·Airlie J McCoyRandy J Read
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Sep 19, 2020·Structure·Vanda LuxVáclav Veverka

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