DesiRNA/CITATION.cff at main · fryzjergda/DesiRNA · GitHub

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# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  DesiRNA: structure-based design of RNA sequences with
  a Monte Carlo approach
message: RNA sequence design software
type: software
authors:
  - given-names: Tomasz K. Wirecki
    email: twirecki@iimcb.gov.pl
    affiliation: >-
      International Institute of Molecular and Cell
      Biology in Warsaw, Warsaw, Poland
    orcid: "https://orcid.org/0000-0001-6539-3640 "
  - given-names: Grzegorz Lach
    email: gel@fuw.edu.pl
    affiliation: >-
      Institute of Theoretical Physics, Faculty of
      Physics (FUW), University of Warsaw, Poland
    orcid: "https://orcid.org/0000-0003-4018-5217"
  - given-names: Farhang Jaryani
    affiliation: >-
      International Institute of Molecular and Cell
      Biology in Warsaw, Warsaw, Poland
    orcid: "https://orcid.org/0000-0001-8374-6681"
  - given-names: Nagendar Goud Badepally
    email: nbadepally@iimcb.gov.pl
    affiliation: >-
      International Institute of Molecular and Cell
      Biology in Warsaw, Warsaw, Poland
    orcid: "https://orcid.org/0000-0003-4364-8811"
  - given-names: S. Naeim Moafinejad
    email: snmoafinejad@iimcb.gov.pl
    affiliation: >-
      International Institute of Molecular and Cell
      Biology in Warsaw, Warsaw, Poland
    orcid: "https://orcid.org/0000-0003-0397-2596"
  - given-names: Gaja Klaudel
    affiliation: >-
      International Institute of Molecular and Cell
      Biology in Warsaw, Warsaw, Poland
  - given-names: Kalina Nec
    email: knec@iimcb.gov.pl
    affiliation: >-
      International Institute of Molecular and Cell
      Biology in Warsaw, Warsaw, Poland
  - given-names: Eugene F. Baulin
    email: ebaulin@iimcb.gov.pl
    affiliation: >-
      International Institute of Molecular and Cell
      Biology in Warsaw, Warsaw, Poland
    orcid: "https://orcid.org/0000-0003-4694-9783"
  - given-names: Janusz M. Bujnicki
    email: janusz@iimcb.gov.pl
    affiliation: >-
      International Institute of Molecular and Cell
      Biology in Warsaw, Warsaw, Poland
    orcid: "https://orcid.org/0000-0001-5758-9416"
identifiers:
  - type: doi
    value: 10.1101/2023.06.04.543636
  - type: url
    value: >-
      https://github.com/fryzjergda/DesiRNA
    description: GitHub repository
abstract: >-
  RNA sequences underpin the formation of complex and diverse structures,
  subsequently governing their respective functional properties. Despite
  the pivotal role RNA sequences play in cellular mechanisms, creating
  optimized sequences that can predictably fold into desired structures
  remains a significant challenge. We have developed DesiRNA, a versatile
  Python-based software tool for RNA sequence design. This program considers
  a comprehensive array of constraints, ranging from secondary structures
  (including pseudoknots) and GC content, to the distribution of dinucleotides
  emulating natural RNAs. Additionally, it factors in the presence or
  absence of specific sequence motifs and prevents or promotes
  oligomerization, thereby ensuring a robust and flexible design process.
  DesiRNA utilizes the Monte Carlo algorithm for the selection and acceptance
  of mutation sites. In tests on the EteRNA benchmark, DesiRNA displayed high
  accuracy and computational efficiency, outperforming most existing RNA
  design programs.

  The DesiRNA software is freely available at
  https://github.com/fryzjergda/DesiRNA
keywords:
  - rna
  - sequence design
  - Eterna benchmark
  - python
license: Apache-2.0