期刊
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
卷 71, 期 -, 页码 1921-1930出版社
INT UNION CRYSTALLOGRAPHY
DOI: 10.1107/S1399004715010846
关键词
phasing; ARCIMBOLDO_BORGES; ab initio; small fragments
资金
- Spanish Ministry of Economy and Competitiveness [BFU2012-35367, BIO2013-49604-EXP]
- Generalitat de Catalunya [2014SGR-997]
- Brazilian Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)
- ICREA Funding Source: Custom
ARCIMBOLDO solves the phase problem at resolutions of around 2 angstrom 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 angstrom 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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