Published in Chem Biol on June 01, 2002
Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis. Biophys J (2008) 1.24
Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition. Nucleic Acids Res (2009) 1.21
Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings. J Biomol NMR (2006) 1.16
Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings. Nat Protoc (2007) 1.16
Ligand-induced changes in 2-aminopurine fluorescence as a probe for small molecule binding to HIV-1 TAR RNA. RNA (2004) 1.11
Solution structure of the HIV-1 frameshift inducing stem-loop RNA. Nucleic Acids Res (2003) 1.10
Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock. J Comput Aided Mol Des (2004) 1.08
Probing Na(+)-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings: new insights into the role of counterions and electrostatic interactions in adaptive recognition. Biochemistry (2007) 1.05
LNA/DNA chimeric oligomers mimic RNA aptamers targeted to the TAR RNA element of HIV-1. Nucleic Acids Res (2004) 0.97
Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition. RNA (2009) 0.96
Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges. J Phys Chem B (2014) 0.95
Monitoring tat peptide binding to TAR RNA by solid-state 31P-19F REDOR NMR. Nucleic Acids Res (2005) 0.94
Discovery of ligands for a novel target, the human telomerase RNA, based on flexible-target virtual screening and NMR. J Med Chem (2008) 0.92
NMR studies of nucleic acid dynamics. J Magn Reson (2013) 0.91
Evidence that electrostatic interactions dictate the ligand-induced arrest of RNA global flexibility. Angew Chem Int Ed Engl (2005) 0.88
Conformational dynamics of RNA-peptide binding: a molecular dynamics simulation study. Biophys J (2005) 0.86
A small-molecule probe induces a conformation in HIV TAR RNA capable of binding drug-like fragments. J Mol Biol (2011) 0.85
Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore. Nucleic Acids Res (2014) 0.82
Novel insights of structure-based modeling for RNA-targeted drug discovery. J Chem Inf Model (2012) 0.82
Identification of biologically active, HIV TAR RNA-binding small molecules using small molecule microarrays. J Am Chem Soc (2014) 0.81
Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings. J Am Chem Soc (2015) 0.78
Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps. J Phys Chem B (2013) 0.78
The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNA. J Comput Aided Mol Des (2007) 0.76
Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales. Biochemistry (2016) 0.75
Inhibition of Bacterial RNase P RNA by Phenothiazine Derivatives. Biomolecules (2016) 0.75
DOCK 6: combining techniques to model RNA-small molecule complexes. RNA (2009) 2.75
Perspectives on NMR in drug discovery: a technique comes of age. Nat Rev Drug Discov (2008) 1.95
A molecular switch underlies a human telomerase disease. Proc Natl Acad Sci U S A (2002) 1.79
Structural and biochemical insights into the dicing mechanism of mouse Dicer: a conserved lysine is critical for dsRNA cleavage. Proc Natl Acad Sci U S A (2008) 1.35
Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA. Chem Biol (2002) 1.30
Locally disordered conformer of the hamster prion protein: a crucial intermediate to PrPSc? Biochemistry (2002) 1.24
NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126. Proc Natl Acad Sci U S A (2003) 1.22
Structure of a construct of a human poly(C)-binding protein containing the first and second KH domains reveals insights into its regulatory mechanisms. J Biol Chem (2008) 1.20
Crystal structure of the first KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.7 A. J Biol Chem (2005) 1.19
Discovery of highly potent and selective small molecule ADAMTS-5 inhibitors that inhibit human cartilage degradation via encoded library technology (ELT). J Med Chem (2012) 1.18
NMR-based characterization of phenothiazines as a RNA binding scaffold. J Am Chem Soc (2004) 1.17
Discovery of thieno[3,2-d]pyrimidine-6-carboxamides as potent inhibitors of SIRT1, SIRT2, and SIRT3. J Med Chem (2013) 1.12
Solution structure of a consensus stem-loop D RNA domain that plays important roles in regulating translation and replication in enteroviruses and rhinoviruses. Biochemistry (2004) 1.08
Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets. J Chem Inf Model (2008) 1.04
PI3K inhibition in neonatal rat brain slices during and after hypoxia reduces phospho-Akt and increases cytosolic cytochrome c and apoptosis. Brain Res Mol Brain Res (2004) 1.02
Pyruvate improves recovery after PARP-1-associated energy failure induced by oxidative stress in neonatal rat cerebrocortical slices. J Cereb Blood Flow Metab (2006) 1.01
Synthesis and testing of a focused phenothiazine library for binding to HIV-1 TAR RNA. Chem Biol (2006) 1.01
Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6 A resolution. Nucleic Acids Res (2007) 0.99
NMR structure of the full-length linear dimer of stem-loop-1 RNA in the HIV-1 dimer initiation site. J Biol Chem (2006) 0.99
Pseudoknot structures with conserved base triples in telomerase RNAs of ciliates. Nucleic Acids Res (2007) 0.96
High-resolution NMR structure of an AT-rich DNA sequence. J Biomol NMR (2002) 0.96
Fragment-based discovery of nonpeptidic BACE-1 inhibitors using tethering. Biochemistry (2009) 0.93
Outcome-related metabolomic patterns from 1H/31P NMR after mild hypothermia treatments of oxygen-glucose deprivation in a neonatal brain slice model of asphyxia. J Cereb Blood Flow Metab (2010) 0.93
Extending the family of UNCG-like tetraloop motifs: NMR structure of a CACG tetraloop from coxsackievirus B3. Biochemistry (2003) 0.92
Discovery of ligands for a novel target, the human telomerase RNA, based on flexible-target virtual screening and NMR. J Med Chem (2008) 0.92
Slow conformational dynamics in the hamster prion protein. Biochemistry (2004) 0.92
NMR structures of loop B RNAs from the stem-loop IV domain of the enterovirus internal ribosome entry site: a single C to U substitution drastically changes the shape and flexibility of RNA. Biochemistry (2004) 0.92
In vivo monitoring of hepatic glutathione in anesthetized rats by 13C NMR. Magn Reson Med (2002) 0.91
Nucleocapsid protein-mediated maturation of dimer initiation complex of full-length SL1 stemloop of HIV-1: sequence effects and mechanism of RNA refolding. Nucleic Acids Res (2007) 0.89
Specific recognition of the C-rich strand of human telomeric DNA and the RNA template of human telomerase by the first KH domain of human poly(C)-binding protein-2. J Biol Chem (2004) 0.89
Detecting ligand binding to a small RNA target via saturation transfer difference NMR experiments in D(2)O and H(2)O. J Am Chem Soc (2002) 0.88
Exogenous ethyl pyruvate versus pyruvate during metabolic recovery after oxidative stress in neonatal rat cerebrocortical slices. Anesthesiology (2007) 0.88
1H nuclear magnetic resonance brain metabolomics in neonatal mice after hypoxia-ischemia distinguished normothermic recovery from mild hypothermia recoveries. Pediatr Res (2013) 0.87
Structure-activity relationships of aminoglycoside-arginine conjugates that bind HIV-1 RNAs as determined by fluorescence and NMR spectroscopy. FEBS Lett (2004) 0.84
Discovery of ligands by a combination of computational and NMR-based screening: RNA as an example target. Methods Enzymol (2005) 0.83
RNA structural motifs that entail hydrogen bonds involving sugar-phosphate backbone atoms of RNA. New J Chem (2010) 0.82
NMR structure of a gemcitabine-substituted model Okazaki fragment. Biochemistry (2002) 0.81
Dynamic NMR structures of [Rp]- and [Sp]-phosphorothioated DNA-RNA hybrids: is flexibility required for RNase H recognition? Biophys J (2003) 0.78
NMR structure of the 3' stem-loop from human U4 snRNA. Nucleic Acids Res (2002) 0.78
Cytochrome c associated apoptosis during ATP recovery after hypoxia in neonatal rat cerebrocortical slices. J Neurochem (2002) 0.78
Temperature control of respiring rat brain slices during high field NMR spectroscopy. Brain Res Brain Res Protoc (2003) 0.78
Using 31P NMR spectroscopy at 14.1 Tesla to investigate PARP-1 associated energy failure and metabolic rescue in cerebrocortical slices. J Bioenerg Biomembr (2004) 0.78
Binding characteristics of small molecules that mimic nucleocapsid protein-induced maturation of stem-loop 1 of HIV-1 RNA. Biochemistry (2010) 0.77
13C NMR metabolomic evaluation of immediate and delayed mild hypothermia in cerebrocortical slices after oxygen-glucose deprivation. Anesthesiology (2013) 0.76
A small molecule, Lys-Ala-7-amido-4-methylcoumarin, facilitates RNA dimer maturation of a stem-loop 1 transcript in vitro: structure-activity relationship of the activator. Biochemistry (2008) 0.76
Optimizing QSAR models for predicting ligand binding to the drug-metabolizing cytochrome P450 isoenzyme CYP2D6. Chem Biol Drug Des (2011) 0.75
Resonance assignment of the first and second KH (hnRNP-K homology) domains of human poly(C)-binding protein-2 (PCBP2). J Biomol NMR (2007) 0.75