Depending on the amount of data to process, file generation may take longer.

If it takes too long to generate, you can limit the data by, for example, reducing the range of years.


Download BibTeX


High-quality, customizable heuristics for RNA 3D structure alignment


[ 1 ] Instytut Informatyki, Wydział Informatyki i Telekomunikacji, Politechnika Poznańska | [ P ] employee

Scientific discipline (Law 2.0)

[2.3] Information and communication technology

Year of publication


Published in


Journal year: 2023 | Journal volume: vol. 39 | Journal number: iss. 5

Article type

scientific article

Publication language


  • RNA
  • sequence-dependent
  • sequence-independent
  • 3D structure alignment
  • metaheuristics
  • genetic algorithm

EN Motivation: Tertiary structure alignment is one of the main challenges in the computer-aided comparative study of molecular structures. Its aim is to optimally overlay the three-dimensional shapes of two or more molecules in space to find the correspondence between their nucleotides. Alignment is the starting point for most algorithms that assess structural similarity or find common substructures. Thus, it has applications in solving a variety of bioinformatics problems, e.g., in the search for structural patterns, structure clustering, identifying structural redundancy, and evaluating the prediction accuracy of 3D models. To date, several tools have been developed to align 3D structures of RNA. However, most of them are not applicable to arbitrarily large structures and do not allow users to parameterize the optimization algorithm. Results: We present two customizable heuristics for flexible alignment of 3D RNA structures, geometric search (GEOS), and genetic algorithm (GENS). They work in sequence-dependent/independent mode and find the suboptimal alignment of expected quality (below a predefined RMSD threshold). We compare their performance with those of state-of-the-art methods for aligning RNA structures. We show the results of quantitative and qualitative tests run for all of these algorithms on benchmark sets of RNA structures.

Date of online publication


Pages (from - to)

btad315-1 - btad315-9





Article: btad315

License type

CC BY (attribution alone)

Open Access Mode

open journal

Open Access Text Version

final published version

Date of Open Access to the publication

in press

Ministry points / journal


Impact Factor

5,8 [List 2022]

This website uses cookies to remember the authenticated session of the user. For more information, read about Cookies and Privacy Policy.