ARCIMBOLDO_LITE: single‐workstation implementation and use. (1st September 2015)
- Record Type:
- Journal Article
- Title:
- ARCIMBOLDO_LITE: single‐workstation implementation and use. (1st September 2015)
- Main Title:
- ARCIMBOLDO_LITE: single‐workstation implementation and use
- Authors:
- Sammito, Massimo
Millán, Claudia
Frieske, Dawid
Rodríguez‐Freire, Eloy
Borges, Rafael J.
Usón, Isabel - 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 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> … (more)
- Is Part Of:
- Acta crystallographica. Volume 71:Part 9(2015:Sep.)
- Journal:
- Acta crystallographica
- Issue:
- Volume 71:Part 9(2015:Sep.)
- Issue Display:
- Volume 71, Issue 9, Part 9 (2015)
- Year:
- 2015
- Volume:
- 71
- Issue:
- 9
- Part:
- 9
- Issue Sort Value:
- 2015-0071-0009-0009
- 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 - Journal URLs:
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http://www.blackwell-synergy.com/loi/ayd ↗
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http://www.iucr.ac.uk/journals/acta/actad.html ↗
http://onlinelibrary.wiley.com/ ↗ - DOI:
- 10.1107/S1399004715010846 ↗
- Languages:
- English
- ISSNs:
- 0907-4449
- Deposit Type:
- Legaldeposit
- View Content:
- Available online (eLD content is only available in our Reading Rooms) ↗
- Physical Locations:
- British Library DSC - 0612.022000
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British Library STI - ELD Digital store - Ingest File:
- 3152.xml