Research Article: Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination

Date Published: April 01, 2018

Publisher: International Union of Crystallography

Author(s): Claudia Millán, Massimo Domenico Sammito, Airlie J. McCoy, Andrey F. Ziem Nascimento, Giovanna Petrillo, Robert D. Oeffner, Teresa Domínguez-Gil, Juan A. Hermoso, Randy J. Read, Isabel Usón.

http://doi.org/10.1107/S2059798318001365

Abstract

ARCIMBOLDO_SHREDDER solves structures using fragments from low-homology models. Search fragments are improved through refinement or trimming against the experimental data. Consistent solutions are combined.

Partial Text

The successful use of distant homologues as search models for molecular replacement (MR) often requires the initial template to undergo a significant degree of improvement as, notwithstanding the overall correct fold or their featuring areas of close geometry, differences may prevent a solution. Model improvement can be contrived by relying on the degree of conservation as implemented in Sculptor (Bunkóczi & Read, 2011 ▸), combining a range of models (Leahy et al., 1992 ▸) as in Ensembler (Bunkóczi et al., 2013 ▸), sampling model deformation along normal modes (McCoy et al., 2013 ▸; Suhre & Sanejouand, 2004 ▸) or modelling within protocols devised for this purpose in Rosetta (DiMaio et al., 2011 ▸), QUARK (Xu & Zhang, 2012 ▸) or I-TASSER (Zhang, 2008 ▸). Fragmenting and reassembling search models has also been explored (Shrestha & Zhang, 2015 ▸).

ARCIMBOLDO_SHREDDER, which seeks to improve fragments from distant homologues through refinement against the experimental data, has been extended to derive models of equal size corresponding to volumes representing structural units centred on each amino acid of the template.

 

Source:

http://doi.org/10.1107/S2059798318001365

 

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