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Journal logoSTRUCTURAL
BIOLOGY

ISSN: 2059-7983

CCP4 Study Weekend 2019

Molecular replacement
Edited by Charles Ballard, Isabel Uson and Randy Read

This virtual issue contains articles from the 2019 CCP4 Study Weekend on molecular replacement.

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Cover illustration: Scheme of the fold-extraction algorithm in ALEPH, fragment-based molecular-replacement software which is optimized for the analysis and extraction of small protein folds by relying on their geometry rather than on their sequence [Medina et al. (2020), Acta Cryst. D76, 193–208].


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Examples are presented of successful data-processing, phasing and refinement strategies for non-merohedral twins, covering the range from minerals to proteins.

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Predicted ab initio protein models from online databases are a useful supplement to the PDB for molecular replacement, but usually require nontrivial processing to succeed.

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Improvements to the sensitivity of the search for suitable molecular-replacement search models in SIMBAD through the use of Phaser and an ensemble-based model database are reported.

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An automatic pipeline based on molecular-replacement phases is described for the automatic crystal structure solution of protein and DNA/RNA molecules.

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Improved coordinate error estimates are proposed for the X-ray and NMR models used for maximum-likelihood-based molecular-replacement phasing.

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ALEPH characterizes the main-chain geometry of small, noncontinuous fragments to flexibly annotate secondary structure, decompose folds, extract libraries and superpose fragments. Secondary and tertiary structure are described through networks of characteristic vectors, which are defined between the centroids of the Cα and carbonyl O atoms in a peptide.

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The software ALIXE, which is available as a standalone program as well as integrated into the ARCIMBOLDO programs, combines partial solutions in reciprocal space to increase the signal and reduce the number of intermediate solutions. Its new implementation is faster and can be used by default in the process of phasing with fragments even on modest hardware.

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When phasing cannot be accomplished from a partial polyalanine starting model, extending the model with side chains in a multi-solution way may succeed. SEQUENCE SLIDER implements this approach for use in ARCIMBOLDO.

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The information content gained by making a diffraction-intensity measurement is a natural criterion for deciding which data make a useful contribution and which can legitimately be omitted from a calculation.

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A novel method for the enhancement of automated protein model building using polypeptide fragments of homologous structures is presented.

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A practical perspective on molecular-replacement (MR) structure-determination pipelines is presented, using PilA1 from Clostridioides difficile as an example of a difficult case. A manual approach informed by the biology of the system under study is described, together with ab initio MR structure determination.

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The solution of coiled-coil crystal structures may be achieved by AMPLE through the use of ensembled ab initio models in molecular replacement. Improvements in ab initio modelling of elongated helices and oligomeric coiled-coils allow AMPLE to solve a greater number of coiled-coil structures and at lower resolution than previously achieved.

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Local error estimates can be used to improve the success of models in molecular replacement.
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