Published in RNA on January 25, 2010
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. Proc Natl Acad Sci U S A (2013) 2.11
Physics-based de novo prediction of RNA 3D structures. J Phys Chem B (2011) 1.21
RNA and protein 3D structure modeling: similarities and differences. J Mol Model (2011) 1.19
Computing the conformational entropy for RNA folds. J Chem Phys (2010) 0.96
The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin. PLoS One (2012) 0.92
New models of Tetrahymena telomerase RNA from experimentally derived constraints and modeling. J Am Chem Soc (2012) 0.86
A conserved RNA pseudoknot in a putative molecular switch domain of the 3'-untranslated region of coronaviruses is only marginally stable. RNA (2011) 0.84
Conjoined use of EM and NMR in RNA structure refinement. PLoS One (2015) 0.81
RNAssess--a web server for quality assessment of RNA 3D structures. Nucleic Acids Res (2015) 0.80
Assembly and activation of a kinase ribozyme. RNA (2010) 0.80
Coarse-grained prediction of RNA loop structures. PLoS One (2012) 0.80
A domain-based model for predicting large and complex pseudoknotted structures. RNA Biol (2012) 0.79
Free energy landscape and multiple folding pathways of an H-type RNA pseudoknot. PLoS One (2015) 0.77
Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel. J Am Chem Soc (2015) 0.76
Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot. Nucleic Acids Res (2017) 0.75
Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction. Nucleic Acids Mol Biol (2012) 0.75
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A (1998) 24.28
Geometric nomenclature and classification of RNA base pairs. RNA (2001) 9.08
Crystal structure of a hepatitis delta virus ribozyme. Nature (1998) 7.07
RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc Natl Acad Sci U S A (2001) 6.58
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA (2008) 5.94
RNA backbone is rotameric. Proc Natl Acad Sci U S A (2003) 5.93
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature (2008) 5.67
Recoding: dynamic reprogramming of translation. Annu Rev Biochem (1996) 4.28
Automated de novo prediction of native-like RNA tertiary structures. Proc Natl Acad Sci U S A (2007) 3.87
Predicting thermodynamic properties of RNA. Methods Enzymol (1995) 3.38
Prediction of RNA secondary structure by free energy minimization. Curr Opin Struct Biol (2006) 3.36
Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Mol Cell (2005) 3.16
Tertiary Motifs in RNA Structure and Folding. Angew Chem Int Ed Engl (1999) 3.15
The building blocks and motifs of RNA architecture. Curr Opin Struct Biol (2006) 2.94
Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J Mol Biol (2000) 2.88
Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA (2008) 2.86
The combination of symbolic and numerical computation for three-dimensional modeling of RNA. Science (1991) 2.66
Stepping through an RNA structure: A novel approach to conformational analysis. J Mol Biol (1998) 2.66
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA (2009) 2.63
Pseudoknots: RNA structures with diverse functions. PLoS Biol (2005) 2.60
Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nat Struct Biol (1999) 2.57
RNA folding causes secondary structure rearrangement. Proc Natl Acad Sci U S A (1998) 2.44
Bridging the gap in RNA structure prediction. Curr Opin Struct Biol (2007) 2.41
Stitching together RNA tertiary architectures. J Mol Biol (1999) 2.40
Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA. Proc Natl Acad Sci U S A (2003) 2.18
A complete conformational map for RNA. J Mol Biol (1999) 2.16
RNA folding energy landscapes. Proc Natl Acad Sci U S A (2000) 2.12
Frameshifting RNA pseudoknots: structure and mechanism. Virus Res (2008) 2.02
RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu Rev Biophys (2008) 2.00
Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics (2005) 1.97
Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nat Struct Mol Biol (2009) 1.88
Heats of the helix-coil transitions of the poly A-poly U complexes. Biopolymers (1968) 1.84
Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. Structure (2009) 1.84
A molecular switch underlies a human telomerase disease. Proc Natl Acad Sci U S A (2002) 1.79
Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Res (2006) 1.75
Structural Insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA. Mol Cell (2009) 1.73
Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting. J Mol Biol (2001) 1.73
RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA. J Biomol Struct Dyn (2008) 1.72
Specific mutations in a viral RNA pseudoknot drastically change ribosomal frameshifting efficiency. Proc Natl Acad Sci U S A (1999) 1.68
Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length. Biophys J (2005) 1.64
Triple-helix structure in telomerase RNA contributes to catalysis. Nat Struct Mol Biol (2008) 1.62
A triple helix within a pseudoknot is a conserved and essential element of telomerase RNA. Mol Cell Biol (2007) 1.61
Functional analysis of the pseudoknot structure in human telomerase RNA. Proc Natl Acad Sci U S A (2005) 1.58
Tertiary structure of an RNA pseudoknot is stabilized by "diffuse" Mg2+ ions. Biochemistry (2007) 1.53
Predicting RNA folding thermodynamics with a reduced chain representation model. RNA (2005) 1.53
Energetics of a strongly pH dependent RNA tertiary structure in a frameshifting pseudoknot. J Mol Biol (2000) 1.52
Predicting structures and stabilities for H-type pseudoknots with interhelix loops. RNA (2009) 1.51
The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain. J Biol Chem (2009) 1.47
Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure. J Mol Biol (2007) 1.45
Tertiary interactions determine the accuracy of RNA folding. J Am Chem Soc (2008) 1.40
Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot. J Mol Biol (2002) 1.31
Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides: a virtual bond model. Biopolymers (1972) 1.31
A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting. Proc Natl Acad Sci U S A (2005) 1.29
YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models. J Chem Theory Comput (2006) 1.27
Annotation of tertiary interactions in RNA structures reveals variations and correlations. RNA (2008) 1.21
Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA. RNA (2007) 1.17
Conservation and diversity among the three-dimensional folds of the Dicistroviridae intergenic region IRESes. J Mol Biol (2007) 1.15
Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins. J Am Chem Soc (2008) 1.13
Mechanistic characterization of the HDV genomic ribozyme: a mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons. Biochemistry (2007) 1.11
Discrete state model and accurate estimation of loop entropy of RNA secondary structures. J Chem Phys (2008) 1.08
Thermodynamic analysis of conserved loop-stem interactions in P1-P2 frameshifting RNA pseudoknots from plant Luteoviridae. Biochemistry (2002) 1.04
Comparative 3-D modeling of tmRNA. BMC Mol Biol (2005) 1.04
The prediction of the wild-type telomerase RNA pseudoknot structure and the pivotal role of the bulge in its formation. J Mol Graph Model (2006) 1.04
An examination of coaxial stacking of helical stems in a pseudoknot motif: the gene 32 messenger RNA pseudoknot of bacteriophage T2. RNA (1999) 1.04
Crystal structure of a luteoviral RNA pseudoknot and model for a minimal ribosomal frameshifting motif. Biochemistry (2005) 1.01
Exploring the complex folding kinetics of RNA hairpins: I. General folding kinetics analysis. Biophys J (2005) 1.01
Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity. J Mol Biol (2007) 0.99
Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions. Nucleic Acids Res (2006) 0.97
Pseudoknot structures with conserved base triples in telomerase RNAs of ciliates. Nucleic Acids Res (2007) 0.96
Structural diversity and isomorphism of hydrogen-bonded base interactions in nucleic acids. J Mol Biol (2003) 0.90
Pseudoknots and the control of protein synthesis. Curr Opin Cell Biol (1990) 0.83
Pairwise coupling analysis of helical junction hydrogen bonding interactions in luteoviral RNA pseudoknots. Biochemistry (2006) 0.81
CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator. Nat Chem Biol (2006) 3.30
Coordination chemistry of bacterial metal transport and sensing. Chem Rev (2009) 2.65
The SmtB/ArsR family of metalloregulatory transcriptional repressors: Structural insights into prokaryotic metal resistance. FEMS Microbiol Rev (2003) 2.51
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 1.88
Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Res (2006) 1.75
Structural determinants of metal selectivity in prokaryotic metal-responsive transcriptional regulators. Biometals (2005) 1.65
Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length. Biophys J (2005) 1.64
A metal-ligand-mediated intersubunit allosteric switch in related SmtB/ArsR zinc sensor proteins. J Mol Biol (2003) 1.61
RNA hairpin-folding kinetics. Proc Natl Acad Sci U S A (2002) 1.60
Predicting RNA folding thermodynamics with a reduced chain representation model. RNA (2005) 1.53
Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte. J Chem Phys (2005) 1.52
Predicting structures and stabilities for H-type pseudoknots with interhelix loops. RNA (2009) 1.51
A nickel-cobalt-sensing ArsR-SmtB family repressor. Contributions of cytosol and effector binding sites to metal selectivity. J Biol Chem (2002) 1.47
Individual metal ligands play distinct functional roles in the zinc sensor Staphylococcus aureus CzrA. J Mol Biol (2005) 1.35
Ion-mediated nucleic acid helix-helix interactions. Biophys J (2006) 1.32
Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot. J Mol Biol (2002) 1.31
A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting. Proc Natl Acad Sci U S A (2005) 1.29
Molecular insights into the metal selectivity of the copper(I)-sensing repressor CsoR from Bacillus subtilis. Biochemistry (2009) 1.29
RNA helix stability in mixed Na+/Mg2+ solution. Biophys J (2007) 1.28
Interplay between manganese and zinc homeostasis in the human pathogen Streptococcus pneumoniae. Metallomics (2011) 1.26
The metalloregulatory zinc site in Streptococcus pneumoniae AdcR, a zinc-activated MarR family repressor. J Mol Biol (2010) 1.25
A U-turn motif-containing stem-loop in the coronavirus 5' untranslated region plays a functional role in replication. RNA (2007) 1.21
Physics-based de novo prediction of RNA 3D structures. J Phys Chem B (2011) 1.21
Structural elements of metal selectivity in metal sensor proteins. Proc Natl Acad Sci U S A (2003) 1.20
Metalloregulatory proteins: metal selectivity and allosteric switching. Biophys Chem (2011) 1.19
Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state. Proc Natl Acad Sci U S A (2009) 1.18
The CRR1 nutritional copper sensor in Chlamydomonas contains two distinct metal-responsive domains. Plant Cell (2010) 1.18
A new structural paradigm in copper resistance in Streptococcus pneumoniae. Nat Chem Biol (2013) 1.17
Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling. Nucleic Acid Ther (2011) 1.16
Unnatural amino acid substitution as a probe of the allosteric coupling pathway in a mycobacterial Cu(I) sensor. J Am Chem Soc (2009) 1.14
Control of copper resistance and inorganic sulfur metabolism by paralogous regulators in Staphylococcus aureus. J Biol Chem (2011) 1.12
Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes. J Mol Biol (2005) 1.09
Putative cis-acting stem-loops in the 5' untranslated region of the severe acute respiratory syndrome coronavirus can substitute for their mouse hepatitis virus counterparts. J Virol (2006) 1.06
A zinc(II)/lead(II)/cadmium(II)-inducible operon from the Cyanobacterium anabaena is regulated by AztR, an alpha3N ArsR/SmtB metalloregulator. Biochemistry (2005) 1.05
Simulating RNA folding kinetics on approximated energy landscapes. J Mol Biol (2008) 1.05
Dual functions of single-stranded DNA-binding protein in helicase loading at the bacteriophage T4 DNA replication fork. J Biol Chem (2004) 1.05
Crystal structure of the zinc-dependent MarR family transcriptional regulator AdcR in the Zn(II)-bound state. J Am Chem Soc (2011) 1.04
Thermodynamic analysis of conserved loop-stem interactions in P1-P2 frameshifting RNA pseudoknots from plant Luteoviridae. Biochemistry (2002) 1.04
A novel cysteine cluster in human metal-responsive transcription factor 1 is required for heavy metal-induced transcriptional activation in vivo. J Biol Chem (2003) 1.03
Salt dependence of nucleic acid hairpin stability. Biophys J (2008) 1.03
Electrostatic free energy landscapes for nucleic acid helix assembly. Nucleic Acids Res (2006) 1.01
Structural and functional characterization of Mycobacterium tuberculosis CmtR, a PbII/CdII-sensing SmtB/ArsR metalloregulatory repressor. Biochemistry (2005) 1.01
Metal site occupancy and allosteric switching in bacterial metal sensor proteins. Arch Biochem Biophys (2011) 1.01
Exploring the complex folding kinetics of RNA hairpins: I. General folding kinetics analysis. Biophys J (2005) 1.01
Coronavirus N protein N-terminal domain (NTD) specifically binds the transcriptional regulatory sequence (TRS) and melts TRS-cTRS RNA duplexes. J Mol Biol (2009) 1.00
Structural lability in stem-loop 1 drives a 5' UTR-3' UTR interaction in coronavirus replication. J Mol Biol (2008) 1.00
The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical. RNA (2006) 0.99
Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity. J Mol Biol (2007) 0.99
Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery. Biochemistry (2012) 0.97
Predicting ribosomal frameshifting efficiency. Phys Biol (2008) 0.96
Mouse hepatitis virus stem-loop 4 functions as a spacer element required to drive subgenomic RNA synthesis. J Virol (2011) 0.96
Computing the conformational entropy for RNA folds. J Chem Phys (2010) 0.96
Understanding and reducing the medication delivery waste via systems mapping and analysis. Health Care Manag Sci (2008) 0.96
Salt contribution to RNA tertiary structure folding stability. Biophys J (2011) 0.96
A novel cyanobacterial SmtB/ArsR family repressor regulates the expression of a CPx-ATPase and a metallothionein in response to both Cu(I)/Ag(I) and Zn(II)/Cd(II). J Biol Chem (2004) 0.95
Structural characterization of distinct alpha3N and alpha5 metal sites in the cyanobacterial zinc sensor SmtB. Biochemistry (2002) 0.95
Allosteric negative regulation of smt O/P binding of the zinc sensor, SmtB, by metal ions: a coupled equilibrium analysis. Biochemistry (2002) 0.95
Spectroscopic studies of the AppA BLUF domain from Rhodobacter sphaeroides: addressing movement of tryptophan 104 in the signaling state. Biochemistry (2009) 0.95
A Cu(I)-sensing ArsR family metal sensor protein with a relaxed metal selectivity profile. Biochemistry (2008) 0.95
Simulations of allosteric motions in the zinc sensor CzrA. J Am Chem Soc (2011) 0.93
Folding thermodynamics of pseudoknotted chain conformations. J Chem Phys (2006) 0.93
Electrostatic free energy landscapes for DNA helix bending. Biophys J (2008) 0.93
Copper transport and trafficking at the host-bacterial pathogen interface. Acc Chem Res (2014) 0.93
Energetics of allosteric negative coupling in the zinc sensor S. aureus CzrA. J Am Chem Soc (2009) 0.93
Salt-dependent folding energy landscape of RNA three-way junction. Biophys J (2010) 0.93
Predicting ion binding properties for RNA tertiary structures. Biophys J (2010) 0.93
Structural insights into homo- and heterotropic allosteric coupling in the zinc sensor S. aureus CzrA from covalently fused dimers. J Am Chem Soc (2006) 0.92
Physical characterization of the manganese-sensing pneumococcal surface antigen repressor from Streptococcus pneumoniae. Biochemistry (2013) 0.92
Mouse hepatitis virus stem-loop 2 adopts a uYNMG(U)a-like tetraloop structure that is highly functionally tolerant of base substitutions. J Virol (2009) 0.91
Statistical thermodynamics for chain molecules with simple RNA tertiary contacts. J Chem Phys (2005) 0.91
Master equation approach to finding the rate-limiting steps in biopolymer folding. J Chem Phys (2003) 0.91
Characterization of a metalloregulatory bismuth(III) site in Staphylococcus aureus pI258 CadC repressor. J Biol Inorg Chem (2002) 0.91
Analyzing the biopolymer folding rates and pathways using kinetic cluster method. J Chem Phys (2003) 0.90
Predicting kissing interactions in microRNA-target complex and assessment of microRNA activity. Nucleic Acids Res (2012) 0.90
Research development of the pathogenesis pathways for neuroschistosomiasis. Neurosci Bull (2010) 0.90
Allosteric inhibition of a zinc-sensing transcriptional repressor: insights into the arsenic repressor (ArsR) family. J Mol Biol (2013) 0.90
Predicting secondary structural folding kinetics for nucleic acids. Biophys J (2010) 0.89
Copper sensing function of Drosophila metal-responsive transcription factor-1 is mediated by a tetranuclear Cu(I) cluster. Nucleic Acids Res (2008) 0.89
Importance of diffuse metal ion binding to RNA. Met Ions Life Sci (2011) 0.88
Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal. RNA (2011) 0.88
Functional transcriptional regulatory sequence (TRS) RNA binding and helix destabilizing determinants of murine hepatitis virus (MHV) nucleocapsid (N) protein. J Biol Chem (2012) 0.87
Mycobacterium tuberculosis NmtR harbors a nickel sensing site with parallels to Escherichia coli RcnR. Biochemistry (2011) 0.87
The CsoR-like sulfurtransferase repressor (CstR) is a persulfide sensor in Staphylococcus aureus. Mol Microbiol (2014) 0.87
Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains. Acta Crystallogr D Biol Crystallogr (2009) 0.86
Exploring the complex folding kinetics of RNA hairpins: II. Effect of sequence, length, and misfolded states. Biophys J (2005) 0.85
Ratiometric pulse-chase amidination mass spectrometry as a probe of biomolecular complex formation. Anal Chem (2011) 0.85
Ion-mediated RNA structural collapse: effect of spatial confinement. Biophys J (2012) 0.85
Kinetics of metal binding by the toxic metal-sensing transcriptional repressor Staphylococcus aureus pI258 CadC. J Inorg Biochem (2006) 0.85
Resonance assignments of the metal sensor CzrA in the apo-, Zn2- and DNA-bound (42 kDa) states. Biomol NMR Assign (2007) 0.85
Co-ordinate synthesis and protein localization in a bacterial organelle by the action of a penicillin-binding-protein. Mol Microbiol (2013) 0.84
Designing a polycationic probe for simultaneous enrichment and detection of microRNAs in a nanopore. ACS Nano (2013) 0.84
Predicting ion-nucleic acid interactions by energy landscape-guided sampling. J Chem Theory Comput (2012) 0.84
A conserved RNA pseudoknot in a putative molecular switch domain of the 3'-untranslated region of coronaviruses is only marginally stable. RNA (2011) 0.84
Ratiometric pulsed alkylation mass spectrometry as a probe of thiolate reactivity in different metalloderivatives of Staphylococcus aureus pI258 CadC. Biochemistry (2004) 0.84
Staphylococcus aureus CstB Is a Novel Multidomain Persulfide Dioxygenase-Sulfurtransferase Involved in Hydrogen Sulfide Detoxification. Biochemistry (2015) 0.84
Kinetic mechanism of conformational switch between bistable RNA hairpins. J Am Chem Soc (2012) 0.83