Practical structure solution with <i>
                     <i>ARCIMBOLDO</i>
                  </i>

Rodríguez, Daniel Salazar; Sammito, Massimo; Meindl, Kathrin; Ilarduya, Iñaki M. de; Potratz, Marianus; Sheldrick, George M.; Usón, Isabel

doi:10.1107/s0907444911056071

Cited by 54 publications

(60 citation statements)

References 18 publications

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“…Attempts at ab initio phasing with small generic fragments and 2.0 Å resolution data sets have been successful in some cases using the program ARCIMBOLDO (Rodríguez et al, 2012;Sammito et al, 2014). 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).…”

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 Cryst Sect 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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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 Cryst Sect D Struct Biol

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“…Although the programs may be run from a command line, younger users find that GUIs such as shelXle [5] for small molecule refinement and hkl2map [6] for experimental phasing of macromolecules are a very convenient way of running SHELX. The SHELX programs have been incorporated into many pipelines for macromolecular structure determination, for example ARCIMBOLDO [7] and AMPLE. [8] …”

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confidence: 99%

Recent developments inSHELX

Sheldrick¹

2013

Acta Cryst Sect A

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“…We have assessed the potential of the ab initio structure-solution program ARCIMBOLDO on protein data complexes, based on the combination of locating small subset DNA -Protein motif fragments with density modification with the program SHELXE in a multisolution frame. [3,4] For proteins, mainchain alpha helices provide the ideal, almost ubiquitous, small fragment to start searches. In the case of DNA complexes, the binding motives constitute a suitable search fragment.…”

mentioning

confidence: 99%

DNA–protein complex structure prediction:ARCIMBOLDOstructure solution with DNA–protein fragment subsets

Pröpper¹,

Meindl²,

Rodríguez³

et al. 2012

Acta Cryst Sect A

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Molecular Replacement (MR) uses a known search model to solve the unknown crystal structure of a related protein, but is dependent on the availability of a model having sufficient structural similarity. Ab initio modelling has developed to the extent that its results can sometimes be used to successfully phase diffraction data. Thus, ab initio models can be tried as search models where structural homologues are not available and experimental phasing is difficult [1]. Our method employs ab initio polyalanine models (or 'decoys'), produced in large numbers then clustered based on the presence of similar core structures. The largest of these clusters is likely to be closest to the native structure [2]. Such ab initio modelling may result in an accurate prediction of the structural core of the target, but with inaccurate loops and termini. We have developed an automated pipeline for the processing of ab initio models for use in MR. We show that clustering of models into ensembles combined with targeted truncation can give a successful result where a single search model would fail. A pipeline has been tested on 296 proteins between 40-120 residues long, using Rosetta to produce 1000 decoys for each target. Ensembles were produced from these decoys, and MR carried out using MrBUMP. A success rate of 42% in this fully automated pipeline was achieved. á-helical proteins are particularly successful (79% success), reflecting the greater accuracy of their modelling ab initio, while all-â protein (5% success) remain problematic. Modelling of side chains onto the ab initio models is sometimes required for success. Successes are achieved at different levels of truncation from <30 to >90% of target sequence in the successful ensemble. Importantly, the likely success or failure of the modelling can be predicted based on characteristics of the protein such as length and secondary structure, and by the convergence of the modelling program to produce a large cluster of models with a similar core structure. Successes at the upper size limit of our test set suggest that larger proteins may sometimes be solved successfully. There are further promising avenues for application of our core methodology to MR cases in which NMR structures or only distant homologues are available. Unlike other computationally intensive methods [3], this method is suitable for modest hardware, allowing for broader adoption. An implementation of the pipeline, AMPLE, has been developed and a beta release version is included in the latest release of the CCP4 software suite. Crystallographic structure solution of DNA -Protein complexes remains a challenging area and requires the combination of theoretical and practical methods. We present a study on a newly developed computational method focused on data from DNA -Protein binding motives. [2]. We have assessed the potential of the ab initio structure-solution program ARCIMBOLDO on protein data complexes, based on the combination of locating small subset DNA -Protein motif fragments with density modification wit...

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Practical structure solution with ARCIMBOLDO

Cited by 54 publications

References 18 publications

An overview of heavy-atom derivatization of protein crystals

An overview of heavy-atom derivatization of protein crystals

Recent developments inSHELX

DNA–protein complex structure prediction:ARCIMBOLDOstructure solution with DNA–protein fragment subsets

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