Geometric properties of nucleic acids with potential for autobuilding

Gruene, Tim; Sheldrick, George M.

doi:10.1107/s0108767310039140

Cited by 15 publications

(20 citation statements)

References 27 publications

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“…Subsequently, another research group also independently determined that C1′ was superior to C4′ for this type of application (Gruene & Sheldrick, 2011; Keating & Pyle, 2010). Thus, for purposes of automated building of RNA into electron density, the P and C1′ atoms appear to be the optimal anchors for a virtual bond system.…”

Section: Pseudo-torsions As Reduced Representations For Rna Conformentioning

confidence: 99%

“…16 a ). The η′ and θ′ torsions are more suitable when interpreting crystallographic density because the C1′ atom is covalently bound to the nucleoside base and therefore can be more easily and accurately located within a low-resolution map (Gruene & Sheldrick, 2011; Keating & Pyle, 2010). …”

Section: The η/θ Formalism As Platform For Innovation In Rna Strucmentioning

confidence: 99%

“…Independent of our research, Gruene & Sheldrick (2011) also used the C1 ‘-based pseudo-torsions to develop a promising approach toward automated building of RNA into electron density. They demonstrated a technique for automatically locating phosphates and bases within density maps, and they showed that η′ and θ′ could be used to assign order and connectivity to these bases and phosphates.…”

Section: The η/θ Formalism As Platform For Innovation In Rna Strucmentioning

confidence: 99%

“…They demonstrated a technique for automatically locating phosphates and bases within density maps, and they showed that η′ and θ′ could be used to assign order and connectivity to these bases and phosphates. The technique identifies phosphates by their strong, tetrahedral-shaped electron density, and finds bases by searching for large, planar ‘ blobs’ of density (Gruene & Sheldrick, 2011). Thus, the combination of this method with our crystallographic model building technique (Keating & Pyle, 2010) holds great promise for fully automated building of RNA structure into electron density.…”

Section: The η/θ Formalism As Platform For Innovation In Rna Strucmentioning

confidence: 99%

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A new way to see RNA

Keating

Humphris

Pyle

2011

Quart. Rev. Biophys.

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Unlike proteins, the RNA backbone has numerous degrees of freedom (eight, if one counts the sugar pucker), making RNA modeling, structure building and prediction a multidimensional problem of exceptionally high complexity. And yet RNA tertiary structures are not infinite in their structural morphology; rather, they are built from a limited set of discrete units. In order to reduce the dimensionality of the RNA backbone in a physically reasonable way, a shorthand notation was created that reduced the RNA backbone torsion angles to two (η and θ, analogous to ϕ and ψ in proteins). When these torsion angles are calculated for nucleotides in a crystallographic database and plotted against one another, one obtains a plot analogous to a Ramachandran plot (the η/θ plot), with highly populated and unpopulated regions. Nucleotides that occupy proximal positions on the plot have identical structures and are found in the same units of tertiary structure. In this review, we describe the statistical validation of the η/θ formalism and the exploration of features within the η/θ plot. We also describe the application of the η/θ formalism in RNA motif discovery, structural comparison, RNA structure building and tertiary structure prediction. More than a tool, however, the η/θ formalism has provided new insights into RNA structure itself, revealing its fundamental components and the factors underlying RNA architectural form.

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Section: Pseudo-torsions As Reduced Representations For Rna Conformentioning

confidence: 99%

Section: The η/θ Formalism As Platform For Innovation In Rna Strucmentioning

confidence: 99%

Section: The η/θ Formalism As Platform For Innovation In Rna Strucmentioning

confidence: 99%

Section: The η/θ Formalism As Platform For Innovation In Rna Strucmentioning

confidence: 99%

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A new way to see RNA

Keating

Humphris

Pyle

2011

Quart. Rev. Biophys.

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“…A few methods have been also developed to facilitate manual model building, such as RCrane (Keating & Pyle, 2010) and Coot (Emsley et al, 2010) Nautilus and ARP/wARP need to determine both the phosphate and base or sugar ring positions to accurately assign the backbone conformers of a single-stranded polynucleotide fragment of a crystal structure model. However, the detection of bases is in general far more difficult than that of phosphates, in particular at low resolution (Hattne & Lamzin, 2008;Gruene & Sheldrick, 2011). In contrast, phenix.find_helices_ strands and phenix.build_rna_helices use a convolution search to find places in the asymmetric unit where an A-RNA or B-DNA helix can be placed (the latter program exclusively builds RNA models).…”

Section: Introductionmentioning

confidence: 99%

BRICKWORXbuilds recurrent RNA and DNA structural motifs into medium and low-resolution electron density maps

Chojnowski¹,

Waleń²,

Piątkowski³

et al. 2015

Acta Cryst Sect A

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Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains singlestranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

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RNA-RNA Interactions

2015

Methods in Molecular Biology

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Geometric properties of nucleic acids with potential for autobuilding

Abstract: Algorithms and geometrical properties are described for the automated building of nucleic acids in experimental electron density.

Cited by 15 publications

References 27 publications

A new way to see RNA

A new way to see RNA

BRICKWORXbuilds recurrent RNA and DNA structural motifs into medium and low-resolution electron density maps

RNA-RNA Interactions

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