Published in J Mol Biol on February 13, 2004
Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein. Proc Natl Acad Sci U S A (2009) 1.33
Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys J (2006) 1.27
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
How binding of small molecule and peptide ligands to HIV-1 TAR alters the RNA motional landscape. Nucleic Acids Res (2009) 1.20
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
Inhibitor-induced structural change in the HCV IRES domain IIa RNA. Proc Natl Acad Sci U S A (2010) 1.10
Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock. J Comput Aided Mol Des (2004) 1.08
γ-AApeptides bind to RNA by mimicking RNA-binding proteins. Org Biomol Chem (2011) 1.06
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
Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets. J Chem Inf Model (2008) 1.04
Optimal drug cocktail design: methods for targeting molecular ensembles and insights from theoretical model systems. J Chem Inf Model (2008) 1.01
Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein. Nucleic Acids Res (2010) 1.00
Inhibition of both HIV-1 reverse transcription and gene expression by a cyclic peptide that binds the Tat-transactivating response element (TAR) RNA. PLoS Pathog (2011) 0.97
Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition. RNA (2009) 0.96
Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection. Drug Discov Today (2010) 0.96
Toward targeting RNA structure: branched peptides as cell-permeable ligands to TAR RNA. ACS Chem Biol (2011) 0.95
Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges. J Phys Chem B (2014) 0.95
Small molecule microarrays of RNA-focused peptoids help identify inhibitors of a pathogenic group I intron. ACS Chem Biol (2009) 0.94
Monitoring tat peptide binding to TAR RNA by solid-state 31P-19F REDOR NMR. Nucleic Acids Res (2005) 0.94
TAR-RNA recognition by a novel cyclic aminoglycoside analogue. Nucleic Acids Res (2006) 0.93
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
Invisible RNA state dynamically couples distant motifs. Proc Natl Acad Sci U S A (2014) 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
Triptolide inhibits human immunodeficiency virus type 1 replication by promoting proteasomal degradation of Tat protein. Retrovirology (2014) 0.82
13C/15N-19F intermolecular REDOR NMR study of the interaction of TAR RNA with Tat peptides. J Am Chem Soc (2010) 0.81
Structure based approaches for targeting non-coding RNAs with small molecules. Curr Opin Struct Biol (2015) 0.79
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
Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones. Nucleic Acids Res (2013) 0.78
An approach to the construction of tailor-made amphiphilic peptides that strongly and selectively bind to hairpin RNA targets. J Am Chem Soc (2009) 0.78
HIV-1 drug discovery: targeting folded RNA structures with branched peptides. Org Biomol Chem (2015) 0.77
Substrate recognition and modification by the nosiheptide resistance methyltransferase. PLoS One (2015) 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
Multivalent Amino Sugars to Recognize Different TAR RNA Conformations. Medchemcomm (2014) 0.75
Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR. Medchemcomm (2017) 0.75
Interactions of protein side chains with RNA defined with REDOR solid state NMR. J Biomol NMR (2011) 0.75
Design of a novel globular protein fold with atomic-level accuracy. Science (2003) 13.06
RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol (2007) 5.33
Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding. Nucleic Acids Res (2005) 2.51
The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res (2007) 2.50
Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA. J Am Chem Soc (2008) 2.26
CBF-1 promotes transcriptional silencing during the establishment of HIV-1 latency. EMBO J (2007) 2.20
Recognition of GU-rich polyadenylation regulatory elements by human CstF-64 protein. EMBO J (2003) 2.01
Establishment of HIV latency in primary CD4+ cells is due to epigenetic transcriptional silencing and P-TEFb restriction. J Virol (2010) 2.01
Spt5 cooperates with human immunodeficiency virus type 1 Tat by preventing premature RNA release at terminator sequences. Mol Cell Biol (2002) 1.82
Structure-activity relationships in purine-based inhibitor binding to HSP90 isoforms. Chem Biol (2004) 1.80
A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T. Environ Microbiol (2010) 1.70
Recruitment of TFIIH to the HIV LTR is a rate-limiting step in the emergence of HIV from latency. EMBO J (2006) 1.68
Protein families and RNA recognition. FEBS J (2005) 1.65
Epigenetic silencing of HIV-1 by the histone H3 lysine 27 methyltransferase enhancer of Zeste 2. J Virol (2011) 1.61
Phosphorylation of the RNA polymerase II carboxyl-terminal domain by CDK9 is directly responsible for human immunodeficiency virus type 1 Tat-activated transcriptional elongation. Mol Cell Biol (2002) 1.61
The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs. Nat Struct Mol Biol (2005) 1.52
High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. J Mol Biol (2006) 1.49
Structure of stem-loop IV of Tetrahymena telomerase RNA. EMBO J (2006) 1.49
The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection. Cell (2007) 1.46
Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein. Proc Natl Acad Sci U S A (2009) 1.33
Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain. Nat Struct Mol Biol (2010) 1.32
A conserved RNA structure within the HCV IRES eIF3-binding site. Nat Struct Biol (2002) 1.31
Structure-based drug design targeting an inactive RNA conformation: exploiting the flexibility of HIV-1 TAR RNA. J Mol Biol (2004) 1.29
An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure. Proteins (2007) 1.28
Riboswitch control of aminoglycoside antibiotic resistance. Cell (2013) 1.28
Structural genomics of infectious disease drug targets: the SSGCID. Acta Crystallogr Sect F Struct Biol Cryst Commun (2011) 1.27
A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Res (2004) 1.27
A knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins. FEBS J (2007) 1.26
NMR studies of dynamics in RNA and DNA by 13C relaxation. Biopolymers (2007) 1.24
Control of HIV latency by epigenetic and non-epigenetic mechanisms. Curr HIV Res (2011) 1.23
Structure-guided peptidomimetic design leads to nanomolar beta-hairpin inhibitors of the Tat-TAR interaction of bovine immunodeficiency virus. Biochemistry (2007) 1.20
How binding of small molecule and peptide ligands to HIV-1 TAR alters the RNA motional landscape. Nucleic Acids Res (2009) 1.20
The C-terminal domains of vertebrate CstF-64 and its yeast orthologue Rna15 form a new structure critical for mRNA 3'-end processing. J Biol Chem (2006) 1.20
Inhibition of the heat shock protein 90 molecular chaperone in vitro and in vivo by novel, synthetic, potent resorcinylic pyrazole/isoxazole amide analogues. Mol Cancer Ther (2007) 1.19
Real-time multidimensional NMR follows RNA folding with second resolution. Proc Natl Acad Sci U S A (2010) 1.18
13C NMR relaxation studies of RNA base and ribose nuclei reveal a complex pattern of motions in the RNA binding site for human U1A protein. J Mol Biol (2005) 1.18
The complex of a designer antibiotic with a model aminoacyl site of the 30S ribosomal subunit revealed by X-ray crystallography. J Am Chem Soc (2003) 1.18
The bacterial ribosome, a promising focus for structure-based drug design. Curr Opin Pharmacol (2002) 1.17
Hydration dependent dynamics in RNA. J Biomol NMR (2009) 1.17
A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III. EMBO J (2004) 1.12
T-cell receptor signaling enhances transcriptional elongation from latent HIV proviruses by activating P-TEFb through an ERK-dependent pathway. J Mol Biol (2011) 1.12
Structural mimicry of retroviral tat proteins by constrained beta-hairpin peptidomimetics: ligands with high affinity and selectivity for viral TAR RNA regulatory elements. J Am Chem Soc (2004) 1.11
Structural basis for contrasting activities of ribosome binding thiazole antibiotics. Chem Biol (2003) 1.10
TAR RNA recognition by a cyclic peptidomimetic of Tat protein. Biochemistry (2005) 1.09
Phosphorylation of CDK9 at Ser175 enhances HIV transcription and is a marker of activated P-TEFb in CD4(+) T lymphocytes. PLoS Pathog (2013) 1.09
The effect of compatible solute ectoines on the structural organization of lipid monolayer and bilayer membranes. Biophys Chem (2010) 1.09
Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock. J Comput Aided Mol Des (2004) 1.08
Structure and stability of wild-type and mutant RNA internal loops from the SL-1 domain of the HIV-1 packaging signal. J Mol Biol (2002) 1.07
How arginine-rich domains coordinate mRNA maturation events. RNA Biol (2007) 1.07
Protein and RNA dynamics play key roles in determining the specific recognition of GU-rich polyadenylation regulatory elements by human Cstf-64 protein. J Mol Biol (2005) 1.07
The solution structure of an essential stem-loop of human telomerase RNA. Nucleic Acids Res (2003) 1.06
Structural basis for stabilization of the tau pre-mRNA splicing regulatory element by novantrone (mitoxantrone). Chem Biol (2009) 1.06
The structure of an enzyme-activating fragment of human telomerase RNA. RNA (2005) 1.06
Engineering RNA-binding proteins for biology. FEBS J (2013) 1.06
γ-AApeptides bind to RNA by mimicking RNA-binding proteins. Org Biomol Chem (2011) 1.06
Validation of automated docking programs for docking and database screening against RNA drug targets. J Med Chem (2004) 1.05
Binding of U1A protein changes RNA dynamics as observed by 13C NMR relaxation studies. Biochemistry (2007) 1.05
Solid-state deuterium NMR studies reveal micros-ns motions in the HIV-1 transactivation response RNA recognition site. J Am Chem Soc (2008) 1.05
Negative elongation factor is required for the maintenance of proviral latency but does not induce promoter-proximal pausing of RNA polymerase II on the HIV long terminal repeat. Mol Cell Biol (2014) 1.03
A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm. Nucleic Acids Res (2009) 1.02
Ectoine and hydroxyectoine inhibit aggregation and neurotoxicity of Alzheimer's beta-amyloid. FEBS Lett (2005) 1.01
Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein. Nucleic Acids Res (2010) 1.00
Novel protein-protein contacts facilitate mRNA 3'-processing signal recognition by Rna15 and Hrp1. J Mol Biol (2010) 1.00
The box H/ACA RNP assembly factor Naf1p contains a domain homologous to Gar1p mediating its interaction with Cbf5p. J Mol Biol (2007) 0.99
Fragment-based hit identification: thinking in 3D. Drug Discov Today (2013) 0.99
Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site. Chem Biol (2006) 0.98
Inhibition of both HIV-1 reverse transcription and gene expression by a cyclic peptide that binds the Tat-transactivating response element (TAR) RNA. PLoS Pathog (2011) 0.97
High-resolution structural validation of the computational redesign of human U1A protein. Structure (2006) 0.96
Methamphetamine activates nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and induces human immunodeficiency virus (HIV) transcription in human microglial cells. J Neurovirol (2012) 0.96
Design of beta-hairpin peptidomimetics that inhibit binding of alpha-helical HIV-1 Rev protein to the rev response element RNA. Angew Chem Int Ed Engl (2007) 0.95
Discovery of a potent CDK2 inhibitor with a novel binding mode, using virtual screening and initial, structure-guided lead scoping. Bioorg Med Chem Lett (2007) 0.94
Structure-based discovery of a new class of Hsp90 inhibitors. Bioorg Med Chem Lett (2005) 0.94
Monitoring tat peptide binding to TAR RNA by solid-state 31P-19F REDOR NMR. Nucleic Acids Res (2005) 0.94
Mitoxantrone analogues as ligands for a stem-loop structure of tau pre-mRNA. J Med Chem (2009) 0.94
Cell-free production of functional Plasmodium falciparum dihydrofolate reductase-thymidylate synthase. Mol Biochem Parasitol (2006) 0.93
Structure of the yeast SR protein Npl3 and Interaction with mRNA 3'-end processing signals. J Mol Biol (2007) 0.93
Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. J Mol Biol (2006) 0.93
Isolated hydatid cyst of kidney. Urology (2009) 0.92
13C relaxation studies of the DNA target sequence for hhai methyltransferase reveal unique motional properties. Biochemistry (2008) 0.91
The structure of a Burkholderia pseudomallei immunophilin-inhibitor complex reveals new approaches to antimicrobial development. Biochem J (2011) 0.91
Theory of nonrigid rotational motion applied to NMR relaxation in RNA. J Phys Chem A (2011) 0.91
Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets. J Chem Inf Comput Sci (2004) 0.90
A new one-pot three-component condensation reaction for the synthesis of 2,3,4,6-tetrasubstituted pyridines. Chem Commun (Camb) (2002) 0.89
Inhibition of beta-amyloid peptide aggregation and neurotoxicity by alpha-d-mannosylglycerate, a natural extremolyte. Peptides (2008) 0.89
Intermediate rate atomic trajectories of RNA by solid-state NMR spectroscopy. J Am Chem Soc (2010) 0.89
A model for C74 addition by CCA-adding enzymes: C74 addition, like C75 and A76 addition, does not involve tRNA translocation. J Biol Chem (2006) 0.89
Design and implementation of an ribonucleic acid (RNA) directed fragment library. J Med Chem (2009) 0.89
Compatible solutes: ectoine and hydroxyectoine improve functional nanostructures in artificial lung surfactants. Biochim Biophys Acta (2011) 0.87
Short-chain fatty acids from periodontal pathogens suppress histone deacetylases, EZH2, and SUV39H1 to promote Kaposi's sarcoma-associated herpesvirus replication. J Virol (2014) 0.87
How a rotavirus hijacks the human protein synthesis machinery. Nat Struct Biol (2002) 0.87