MCQ4Structures to compute similarity of molecule structures

Żok, Tomasz; Popenda, Mariusz; Szachniuk, Marta

doi:10.1007/s10100-013-0296-5

Cited by 40 publications

(45 citation statements)

References 24 publications

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“…The Clash Score as evaluated by MolProbity is also used as a control measurement for the quality of the geometric parameters of the models (Chen et al 2010). Additionally, MCQ (Mean of Circular Quantities) score (Zok et al 2014) was added as a reference to assess prediction in terms of torsion angle space. MCQ measures the dissimilarity between structures taking into account rotatable bonds and sugar pucker.…”

Section: Assessment Methodsmentioning

confidence: 99%

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Miao

Adamiak

Blanchet

et al. 2015

RNA

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This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with limited or no homology with previously solved RNA molecules. A lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, and AMBER refinement. Some groups derived models using data from state-of-the-art chemicalmapping methods (SHAPE, DMS, CMCT, and mutate-and-map). The comparisons between the predictions and the three subsequently released crystallographic structures, solved at diffraction resolutions of 2.5-3.2 Å, were carried out automatically using various sets of quality indicators. The comparisons clearly demonstrate the state of present-day de novo prediction abilities as well as the limitations of these state-of-the-art methods. All of the best prediction models have similar topologies to the native structures, which suggests that computational methods for RNA structure prediction can already provide useful structural information for biological problems. However, the prediction accuracy for non-Watson-Crick interactions, key to proper folding of RNAs, is low and some predicted models had high Clash Scores. These two difficulties point to some of the continuing bottlenecks in RNA structure prediction. All submitted models are available for download at http://ahsoka.u-strasbg .fr/rnapuzzles/.

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Section: Assessment Methodsmentioning

confidence: 99%

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Miao

Adamiak

Blanchet

et al. 2015

RNA

Self Cite

180

201

View full text Add to dashboard Cite

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“…In the future, its resources will be increased by further data and tools for RNA bioinformatics researchers. Notably, the platform will be enriched, among other things, with systems analysing the structure in the space of torsional angles [57], searching for similar fragments [54], supporting the study of nucleic acids quadruplexes, and identifying a consensus structure in a set of multiple RNA models. The ambition of the author of the RNApolis project is for the platform to become a virtual laboratory for the analysis of RNA structures enabling multidirectional bioinformatics research.…”

Section: Discussionmentioning

confidence: 99%

RNApolis: Computational Platform for RNA Structure Analysis

Szachniuk

2019

Foundations of Computing and Decision Sciences

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In the 1970s, computer scientists began to engage in research in the field of structural biology. The first structural databases, as well as models and methods supporting the analysis of biomolecule structures, started to be created. RNA was put at the centre of scientific interest quite late. However, more and more methods dedicated to this molecule are currently being developed. This paper presents RNApolis - a new computing platform, which offers access to seven bioinformatic tools developed to support the RNA structure study. The set of tools include a structural database and systems for predicting, modelling, annotating and evaluating the RNA structure. RNApolis supports research at different structural levels and allows the discovery, establishment, and validation of relationships between the primary, secondary and tertiary structure of RNAs. The platform is freely available at http://rnapolis.pl

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“…It is a known fact that the similarity in structure (cf. (Zok et al, 2014) for information about structural similarities) of molecules, like proteins or RNAs, highly correlates with sequence similarities, under assumption that all of the structures compared where obtained under similar conditions. Similar conditions are important from the perspective of thermodynamics -changes in conditions are the driving force of folding and unfolding.…”

Section: Introductionmentioning

confidence: 99%

StructAnalyzer - a tool for sequence vs. structure similarity analysis

Wiedemann

Miłostan

2017

Acta Biochim Pol

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In the world of RNAs and proteins, similarities at the level of primary structures of two comparable molecules usually correspond to structural similarities at the tertiary level. In other words, measures of sequence and structure similarities are in general correlated - a high value of sequence similarity imposes a high value of structural similarity. However, important exceptions that stay in contrast to this general rule can be identified. It is possible to find similar structures with very different sequences, as well as similar sequences with very different structures. In this paper, we focus our attention on the latter case and propose a tool, called StructAnalyzer, supporting analysis of relations between the sequence and structure similarities. Recognition of tertiary structure diversity of molecules with very similar primary structures may be the key for better understanding of mechanisms influencing folding of RNAs or proteins, and as a result for better understanding of their function. StructAnalyzer allows exploration and visualization of structural diversity in relation to sequence similarity. We show how this tool can be used to screen RNA structures in Protein Data Bank (PDB) for sequences with structural variants.

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MCQ4Structures to compute similarity of molecule structures

Cited by 40 publications

References 24 publications

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

RNApolis: Computational Platform for RNA Structure Analysis

StructAnalyzer - a tool for sequence vs. structure similarity analysis

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