Genus for biomolecules

Rubach, Paweł; Zajac, S.; Jastrzębski, Borys; Sułkowska, Joanna I.; Sułkowski, Piotr

doi:10.1093/nar/gkz845

Cited by 9 publications

(6 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…protein backbone) threads through itself. Exploring them is aided by protein-centered computational tools ( 17 , 18 ), which can be applied to RNA, although not incorporating base-pairing critical in RNA folding. Knot-like folds have been observed in viral exoribonuclease-resistant RNAs ( 19 , 20 ) and SARS-CoV-2 ribosomal frameshifting element (FSE) ( 11 , 21 ).…”

Section: Introductionmentioning

confidence: 99%

RNAspider: a webserver to analyze entanglements in RNA 3D structures

Luwanski

Hlushchenko

Popenda

et al. 2022

Nucleic Acids Research

View full text Add to dashboard Cite

Advances in experimental and computational techniques enable the exploration of large and complex RNA 3D structures. These, in turn, reveal previously unstudied properties and motifs not characteristic for small molecules with simple architectures. Examples include entanglements of structural elements in RNA molecules and knot-like folds discovered, among others, in the genomes of RNA viruses. Recently, we presented the first classification of entanglements, determined by their topology and the type of entangled structural elements. Here, we introduce RNAspider – a web server to automatically identify, classify, and visualize primary and higher-order entanglements in RNA tertiary structures. The program applies to evaluate RNA 3D models obtained experimentally or by computational prediction. It supports the analysis of uncommon topologies in the pseudoknotted RNA structures. RNAspider is implemented as a publicly available tool with a user-friendly interface and can be freely accessed at https://rnaspider.cs.put.poznan.pl/.

show abstract

Section: Introductionmentioning

confidence: 99%

RNAspider: a webserver to analyze entanglements in RNA 3D structures

Luwanski

Hlushchenko

Popenda

et al. 2022

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Full details on how the genus of a structure is defined and computed can be found in [ 19 , 20 , 55 ]. The Genus for Biomolecules database [ 56 , 57 ] at https://genus.fuw.edu.pl permits to compute the genus trace plot of a molecule. We defined a Python script implementing the algorithm presented in [ 58 ], which is able to compute the genus of a structure.…”

Section: Methodsmentioning

confidence: 99%

Automatic generation of pseudoknotted RNAs taxonomy

2023

View full text Add to dashboard Cite

Background The ability to compare RNA secondary structures is important in understanding their biological function and for grouping similar organisms into families by looking at evolutionarily conserved sequences such as 16S rRNA. Most comparison methods and benchmarks in the literature focus on pseudoknot-free structures due to the difficulty of mapping pseudoknots in classical tree representations. Some approaches exist that permit to cluster pseudoknotted RNAs but there is not a general framework for evaluating their performance. Results We introduce an evaluation framework based on a similarity/dissimilarity measure obtained by a comparison method and agglomerative clustering. Their combination automatically partition a set of molecules into groups. To illustrate the framework we define and make available a benchmark of pseudoknotted (16S and 23S) and pseudoknot-free (5S) rRNA secondary structures belonging to Archaea, Bacteria and Eukaryota. We also consider five different comparison methods from the literature that are able to manage pseudoknots. For each method we clusterize the molecules in the benchmark to obtain the taxa at the rank phylum according to the European Nucleotide Archive curated taxonomy. We compute appropriate metrics for each method and we compare their suitability to reconstruct the taxa.

show abstract

“…In this spirit, in 2002 Orland and Zee [27] proposed a method for predicting the tertiary structure of RNA based on such a matrix theory. Indeed, the usage of diagrams to describe secondary and tertiary RNA structures is actually a common practice, as testified by a large number of representations, which one can find in the literature [27][28][29][30][31][32][33][34][35].…”

Section: Rna Folding Problemmentioning

confidence: 99%

Feynman Diagrams beyond Physics: From Biology to Economy

Cangiotti

2024

Mathematics

View full text Add to dashboard Cite

Feynman diagrams represent one of the most powerful and fascinating tools developed in theoretical physics in the last century. Introduced within the framework of quantum electrodynamics as a suitable method for computing the amplitude of a physical process, they rapidly became a fundamental mathematical object in quantum field theory. However, their abstract nature seems to suggest a wider usage, which actually exceeds the physical context. Indeed, as mathematical objects, they could simply be considered graphs that depict not only physical quantities but also biological or economic entities. We survey the analytical and algebraic properties of such diagrams to understand their utility in several areas of science, eventually providing some examples of recent applications.

show abstract

Genus for biomolecules

Cited by 9 publications

References 31 publications

RNAspider: a webserver to analyze entanglements in RNA 3D structures

RNAspider: a webserver to analyze entanglements in RNA 3D structures

Automatic generation of pseudoknotted RNAs taxonomy

Feynman Diagrams beyond Physics: From Biology to Economy

Contact Info

Product

Resources

About