Molecular modeling by means of docking and molecular dynamics (MD) has become an\nintegral part of early drug discovery projects, enabling the screening and enrichment of large libraries\nof small molecules. In the past decades, special emphasis was drawn to nucleic acid (NA)-based\nmolecules in the fields of therapy, diagnosis, and drug delivery. Research has increased dramatically\nwith the advent of the SELEX (systematic evolution of ligands by exponential enrichment) technique,\nwhich results in single-stranded DNA or RNA sequences that bind with high affinity and specificity to\ntheir targets. Herein, we discuss the role and contribution of docking and MD to the development and\noptimization of new nucleic acid-based molecules. This review focuses on the different approaches\ncurrently available for molecular modeling applied to NA interaction with proteins. We discuss\ntopics ranging from structure prediction to docking and MD, highlighting their main advantages and\nlimitations and the influence of flexibility on their calculations.
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