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Molecular recognition of RNA: challenges for modelling interactions and plasticity
Author(s) -
Fulle Simone,
Gohlke Holger
Publication year - 2009
Publication title -
journal of molecular recognition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.401
H-Index - 79
eISSN - 1099-1352
pISSN - 0952-3499
DOI - 10.1002/jmr.1000
Subject(s) - rna , computational biology , molecular dynamics , nucleic acid , docking (animal) , protein–ligand docking , molecular recognition , nucleic acid structure , computer science , chemistry , nanotechnology , biology , biochemical engineering , molecule , biochemistry , materials science , computational chemistry , virtual screening , engineering , gene , medicine , nursing , organic chemistry
There is growing interest in molecular recognition processes of RNA because of RNA's widespread involvement in biological processes. Computational approaches are increasingly used for analysing and predicting binding to RNA, fuelled by encouraging progress in developing simulation, free energy and docking methods for nucleic acids. These developments take into account challenges regarding the energetics of RNA–ligand binding, RNA plasticity, and the presence of water molecules and ions in the binding interface. Accordingly, we will detail advances in force field and scoring function development for molecular dynamics (MD) simulations, free energy computations and docking calculations of nucleic acid complexes. Furthermore, we present methods that can detect moving parts within RNA structures based on graph‐theoretical approaches or normal mode analysis (NMA). As an example of the successful use of these developments, we will discuss recent structure‐based drug design approaches that focus on the bacterial ribosomal A‐site RNA as a drug target. Copyright © 2009 John Wiley & Sons, Ltd.