<i>AMPLE</i>: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed<i>ab initio</i>models

Bibby, Jaclyn; Keegan, Ronan; Mayans, Olga; Winn, Martyn; Rigden, Daniel J.

doi:10.1107/s0907444912039194

Cited by 116 publications

(179 citation statements)

References 44 publications

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“…This Nipah virus structure was eventually determined by using the automated pipeline AMPLE (26), which performs molecular replacement searches using ab initio models. Here, AMPLE was used differently: to cluster and truncate a set of 100 comparative models for Nipah virus P that were generated by ROSETTA (27), using mumps virus P as a template (PDB, 4EIJ; 26% identical in sequence to Nipah virus) (16,17).…”

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confidence: 99%

Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain

Bruhn

Barnett

Bibby

et al. 2014

J Virol

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eThe Nipah virus phosphoprotein (P) is multimeric and tethers the viral polymerase to the nucleocapsid. We present the crystal structure of the multimerization domain of Nipah virus P: a long, parallel, tetrameric, coiled coil with a small, ␣-helical cap structure. Across the paramyxoviruses, these domains share little sequence identity yet are similar in length and structural organization, suggesting a common requirement for scaffolding or spatial organization of the functions of P in the virus life cycle.

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confidence: 99%

Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain

Bruhn

Barnett

Bibby

et al. 2014

J Virol

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“…Ensembles of ab initio models obtained from ROSETTA/QUARK have also been fruitful for lower resolution data sets using the program AMPLE (Bibby et al, 2012). However, in many cases crystals do not give high enough resolution diffraction for these methods to work, particularly if they are being applied to challenging structures such as large complexes or membrane proteins.…”

Section: Methods For Obtaining Phases Without Additional Experimentalmentioning

confidence: 99%

An overview of heavy-atom derivatization of protein crystals

Pike

Garman

Krojer

et al. 2016

Acta Crystallogr D Struct Biol

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Heavy-atom derivatization is one of the oldest techniques for obtaining phase information for protein crystals and, although it is no longer the first choice, it remains a useful technique for obtaining phases for unknown structures and for low-resolution data sets. It is also valuable for confirming the chain trace in lowresolution electron-density maps. This overview provides a summary of the technique and is aimed at first-time users of the method. It includes guidelines on when to use it, which heavy atoms are most likely to work, how to prepare heavy-atom solutions, how to derivatize crystals and how to determine whether a crystal is in fact a derivative.

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“…Modeling can be applied to increase the convergence when starting from a poor template from a distant homolog (DiMaio et al, 2011). Furthermore if de novo structure prediction can reach enough accuracy, this approach provides an ab initio method (Bibby et al, 2012).…”

Section: Non Crystallographic Symmetry and Molecular Replacementmentioning

confidence: 99%

Crystallographic structure solution

Millán¹,

Usón²

2015

Arbor

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The three-dimensional view of molecules at the atomic level provided by X-ray crystallography is not only extremely informative but is also easily and intuitively understood by humans, who very much rely on their vision. However, unlike microscopy, this technique does not directly yield an image. The structural model cannot be directly calculated from the diffraction data, as only the intensities of scattered beams and not their phases are experimentally accessible. In order to obtain the 3-dimensional structure phases have to be obtained by either additional experimental or computational methods. This is known as the phase problem in crystallography. In this manuscript we provide an overview of major milestones along the quest for the lost phases.KEYWORDS: phase problem; constraints; structure factors; Fourier maps; search; minimization; maximum-likelihood; optimization; restraints; X-rays. RESUMEN: La cristalografía proporciona una visión tridimensional de las moléculas a un nivel de detalle atómico, que no sólo resulta muy informativa sino que además puede ser fácil e intuitivamente comprendida por seres tan predominantemente visuales como solemos ser los humanos. Sin embargo, al contrario que la microscopía, esta técnica no ofrece directamente una imagen y el modelo estructural no puede calcularse directamente a partir de los datos de difracción, ya que solamente las intensidades de los rayos difractados y no sus fases son accesibles a la medida experimental. Para determinar la estructura tridimensional las fases deben ser obtenidas por medio de métodos adicionales, bien experimentales o computacionales. Esto constituye el problema de la fase en cristalografía. En este artículo ofreceremos una visión general de los principales hitos en la búsqueda de las fases perdidas.PALABRAS CLAVE: problema de la fase; constricciones; factores de estructura; mapas de Fourier; métodos de búsqueda; minimización; máxima verosimilitud; optimización; restricciones; rayos-X.

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AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computedab initiomodels

Cited by 116 publications

References 44 publications

Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain

Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain

An overview of heavy-atom derivatization of protein crystals

Crystallographic structure solution

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