Primary Citation PubMed: 17411085
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Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs.
(2009) J Chem Theory Comput 5
PubMed: 20090924 | PubMedCentral: PMC2807739 | DOI: 10.1021/ct800540c
Figure 8 5′iC G 3′/3′iGA5′, imino GA stacked on iCiG in 5′GGiC GA iGCC3′/3′CCiG AG iCGG5′ ( 2O83 ) after minimization with amber99 force... field.
Colored nucleotides in a−d are the loop regions of NMR structures of 2O81 , 1MIS , 2O83 , and 1YFV , respectively, from the PDB.
PDB IDs of (5′GGC GA GCC3′) 2 and (5′GGiC GA iGCC3′) 2 are 1YFV and 2O83 , respectively.
Publication Year: 2009
Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA.
(2014) J Chem Theory Comput 10
PubMed: 24803859 | PubMedCentral: PMC3985902 | DOI: 10.1021/ct400861g
38 They used four solution structures (PDB numbers 1MIS, 2O83, 2O81, and 1YFV), 22 , 44 , 45 and they used thermodynamic integration to calculate free energy differences.
Publication Year: 2014
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