ModXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields.

ABSTRACT: Modified nucleic acids have surged as a popular therapeutic route, emphasizing the importance of nucleic acid research in drug discovery and development. Beyond well-known RNA vaccines, antisense oligonucleotides and aptamers can incorporate various modified nucleic acids to target specific biomolecules for various therapeutic activities. Molecular dynamics simulations can accelerate the design and development of these systems with noncanonical nucleic acids by observing intricate dynamic properties and relative stability on the all-atom level. However, modeling these modified systems is challenging due to the time and resources required to parametrize components outside default force field parameters. Here, we present modXNA, a tool to derive and build modified nucleotides for use with Am

SUBMITTER: Love O 

PROVIDER: S-EPMC11562377 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature