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RNA challenges for computational chemists.
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J Am Chem Soc. 2001 Feb 21;123(7):1267-74. doi: 10.1021/ja002623i.
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The energetics of small internal loops in RNA.
Biopolymers. 1999;52(4):157-67. doi: 10.1002/1097-0282(1999)52:4<157::AID-BIP1001>3.0.CO;2-E.
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Solution structure of an RNA internal loop with three consecutive sheared GA pairs.
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Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases.
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2
Extending density functional theory with near chemical accuracy beyond pure water.
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Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides.
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RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
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Physics-based all-atom modeling of RNA energetics and structure.
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Blind tests of RNA nearest-neighbor energy prediction.
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RNA design rules from a massive open laboratory.
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Computational approaches to predicting the impact of novel bases on RNA structure and stability.
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10
Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position.
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The thermodynamics of DNA structural motifs.
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An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots.
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Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
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Pronounced instability of tandem IU base pairs in RNA.
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A guide to ions and RNA structure.
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