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CITATION.cff
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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: >-
fingeRNAt—A novel tool for high-throughput analysis
of nucleic acid-ligand interactions: pymol plugin
message: pymol plugin for fingeRNAt
type: software
authors:
- given-names: "Natalia A. Szulc "
email: nszulc@iimcb.gov.pl
affiliation: >-
International Institute of Molecular and Cell
Biology in Warsaw, Warsaw, Poland
orcid: "https://orcid.org/0000-0002-2991-3634"
- given-names: Zuzanna Mackiewicz
email: zmackiewicz@iimcb.gov.pl
affiliation: >-
International Institute of Molecular and Cell
Biology in Warsaw, Warsaw, Poland
orcid: "https://orcid.org/0000-0003-1654-9025"
- orcid: "https://orcid.org/0000-0002-6633-165X"
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"
given-names: Filip Stefaniak
affiliation: >-
International Institute of Molecular and Cell
Biology in Warsaw, Warsaw, Poland
email: fstefaniak@iimcb.gov.pl
identifiers:
- type: doi
value: 10.1371/journal.pcbi.1009783
- type: url
value: >-
https://github.com/filipsPL/fingernat-pymol-plugin
description: GitHub repository
- type: doi
value: 10.5281/zenodo.7341533
description: Zenodo github repository
repository-code: "https://github.com/filipsPL/fingernat-pymol-plugin"
url: "https://github.com/n-szulc/fingeRNAt/"
abstract: >-
Computational methods play a pivotal role in drug
discovery and are widely applied in virtual
screening, structure optimization, and compound
activity profiling. Over the last decades, almost
all the attention in medicinal chemistry has been
directed to protein-ligand binding, and
computational tools have been created with this
target in mind. With novel discoveries of
functional RNAs and their possible applications,
RNAs have gained considerable attention as
potential drug targets. However, the availability
of bioinformatics tools for nucleic acids is
limited. Here, we introduce fingeRNAt—a software
tool for detecting non-covalent interactions formed
in complexes of nucleic acids with ligands. The
program detects nine types of interactions: (i)
hydrogen and (ii) halogen bonds, (iii)
cation-anion, (iv) pi-cation, (v) pi-anion, (vi)
pi-stacking, (vii) inorganic ion-mediated, (viii)
water-mediated, and (ix) lipophilic interactions.
However, the scope of detected interactions can be
easily expanded using a simple plugin system. In
addition, detected interactions can be visualized
using the associated PyMOL plugin, which
facilitates the analysis of medium-throughput
molecular complexes. Interactions are also encoded
and stored as a bioinformatics-friendly Structural
Interaction Fingerprint (SIFt)—a binary string
where the respective bit in the fingerprint is set
to 1 if a particular interaction is present and to
0 otherwise. This output format, in turn, enables
high-throughput analysis of interaction data using
data analysis techniques. We present applications
of fingeRNAt-generated interaction fingerprints for
visual and computational analysis of RNA-ligand
complexes, including analysis of interactions
formed in experimentally determined RNA-small
molecule ligand complexes deposited in the Protein
Data Bank. We propose interaction fingerprint-based
similarity as an alternative measure to RMSD to
recapitulate complexes with similar interactions
but different folding. We present an application of
interaction fingerprints for the clustering of
molecular complexes. This approach can be used to
group ligands that form similar binding networks
and thus have similar biological properties. The
fingeRNAt software is freely available at
https://github.com/n-szulc/fingeRNAt.
keywords:
- rna
- small molecules
- non-covalent interactions
- interaction fingerprint
- python
- drug design
license: Apache-2.0