E. F. Baulin, M. A. Roytberg, “Stem multiplets: a new approach to the description of tertiary RNA motifs”, Mat. Biolog. Bioinform., 2015, Volume 10, Issue 1,Pages <nobr>54–59</nobr>

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Mat. Biolog. Bioinform., 2015 Volume 10, Issue 1, Pages 54–59 (Mi mbb211)

Bioinformatics

Stem multiplets: a new approach to the description of tertiary RNA motifs

E. F. Baulin^abc, M. A. Roytberg^cda

^a Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia
^b Educational Center of Mathematical Biology, Pushchino State Institute of Natural Sciences, Pushchino, Moscow region, 142290, Russia
^c Faculty of Computer Science, National Research University “Higher School of Economics”, Moscow, 101000, Russia
^d Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow region, 141700, Russia

Abstract: We present an approach allowing one to describe complex fragments of RNA tertiary structure. The approach is based on the definition of a stem multiplet, i.e. a structural element formed by two or more interacting stems. Using previously developed database of RNA structures (http://server3.lpm.org.ru/urs/) we have revealed all stem multiplets presented in the PDB database.

Key words: 3D RNA structure, multiplet, stem, pseudoknot, link, graph.

UDC: 577.214.5

Received 28.11.2014, Published 06.02.2015

DOI: 10.17537/2015.10.54

© Steklov Math. Inst. of RAS, 2024