Published in J Am Chem Soc on April 08, 2013
Identification of a juxtamembrane mechanosensitive domain in the platelet mechanosensor glycoprotein Ib-IX complex. Blood (2014) 1.03
Construction of RNA-Quantum Dot Chimera for Nanoscale Resistive Biomemory Application. ACS Nano (2015) 0.83
Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing. RNA (2014) 0.81
Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations. BMC Bioinformatics (2015) 0.80
Many-body effect in ion binding to RNA. J Chem Phys (2014) 0.78
May the Best Molecule Win: Competition ESI Mass Spectrometry. Int J Mol Sci (2015) 0.77
Nanomanipulation of single RNA molecules by optical tweezers. J Vis Exp (2014) 0.75
On the conformational stability of the smallest RNA kissing complexes maintained through two G·C base pairs. Biochem Biophys Res Commun (2017) 0.75
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J Chem Theory Comput (2008) 34.90
Crystal structure of the ribosome at 5.5 A resolution. Science (2001) 18.21
Stability of ribonucleic acid double-stranded helices. J Mol Biol (1974) 16.35
Structures of the bacterial ribosome at 3.5 A resolution. Science (2005) 12.63
Reversible unfolding of single RNA molecules by mechanical force. Science (2001) 8.14
RNA structure prediction. Annu Rev Biophys Biophys Chem (1988) 5.75
Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys (2008) 3.87
Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid. Science (2006) 3.49
Predicting thermodynamic properties of RNA. Methods Enzymol (1995) 3.38
Optical-trap force transducer that operates by direct measurement of light momentum. Methods Enzymol (2003) 2.86
Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. J Chem Phys (2005) 2.76
A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol (2008) 2.53
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res (2009) 2.49
Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA. J Am Chem Soc (2000) 2.24
Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods. Biophys J (2005) 1.86
R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments. Nucleic Acids Res (2011) 1.64
The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. Acc Chem Res (2011) 1.51
A retroviral RNA kissing complex containing only two G.C base pairs. Proc Natl Acad Sci U S A (2000) 1.50
Analysis of noncovalent complexes of DNA and RNA by mass spectrometry. Chem Rev (2001) 1.36
Parameters of monovalent ions in the AMBER-99 forcefield: assessment of inaccuracies and proposed improvements. J Phys Chem B (2007) 1.31
Ribosome structure and dynamics during translocation and termination. Annu Rev Biophys (2010) 1.31
Unusual mechanical stability of a minimal RNA kissing complex. Proc Natl Acad Sci U S A (2006) 1.29
Folding and unfolding single RNA molecules under tension. Curr Opin Chem Biol (2008) 1.26
Association of complementary oligoribonucleotides in aqueous solution. Biochemistry (1968) 1.23
Identification of a high affinity nucleocapsid protein binding element within the Moloney murine leukemia virus Psi-RNA packaging signal: implications for genome recognition. J Mol Biol (2001) 1.19
Direct mass spectrometric determination of the stoichiometry and binding affinity of the complexes between nucleocapsid protein and RNA stem-loop hairpins of the HIV-1 Psi-recognition element. Biochemistry (2003) 1.15
Determination of thermodynamics and kinetics of RNA reactions by force. Q Rev Biophys (2006) 1.13
Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. J Chem Phys (2011) 1.08
Dissecting the protein-RNA and RNA-RNA interactions in the nucleocapsid-mediated dimerization and isomerization of HIV-1 stemloop 1. J Mol Biol (2006) 1.03
The dynamic structural basis of differential enhancement of conformational stability by 5'- and 3'-dangling ends in RNA. Biochemistry (2008) 1.02
Understanding the isomerization of the HIV-1 dimerization initiation domain by the nucleocapsid protein. J Mol Biol (2007) 0.97
Studies of trinucleotide conformations. Role of guanine residues in an oligonucleotide chain. Biochemistry (1969) 0.97
Predicting and modeling RNA architecture. Cold Spring Harb Perspect Biol (2011) 0.95
Structural probing of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands. Nucleic Acids Res (2008) 0.94
Inhibitory effects of archetypical nucleic acid ligands on the interactions of HIV-1 nucleocapsid protein with elements of Psi-RNA. Nucleic Acids Res (2006) 0.93
Mechanical unfolding of two DIS RNA kissing complexes from HIV-1. J Mol Biol (2009) 0.86
Noncovalent probes for the investigation of structure and dynamics of protein-nucleic acid assemblies: the case of NC-mediated dimerization of genomic RNA in HIV-1. Biopolymers (2009) 0.86
A uniform mechanism correlating dangling-end stabilization and stacking geometry. Biochemistry (2005) 0.85
Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations. Proc Natl Acad Sci U S A (2012) 0.82
Probing anomalous structural features in polypurine tract-containing RNA-DNA hybrids with neomycin B. Biochemistry (2009) 0.82
MS analysis of nucleic acids in the post-genomic era. Anal Chem (2011) 0.78
A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles. Mol Biol Cell (2002) 5.34
Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell (2002) 4.39
The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res (2010) 3.42
Genome-wide analysis identifies interleukin-10 mRNA as target of tristetraprolin. J Biol Chem (2008) 2.38
The Alzheimer's peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study. J Mol Biol (2007) 2.35
Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 TAT peptide across lipid membranes. Proc Natl Acad Sci U S A (2007) 1.98
Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling. Methods Mol Biol (2008) 1.74
An in-depth map of polyadenylation sites in cancer. Nucleic Acids Res (2012) 1.71
Caspase-mediated cleavage of HuR in the cytoplasm contributes to pp32/PHAP-I regulation of apoptosis. J Cell Biol (2008) 1.63
Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Biophys J (2007) 1.61
Cavities determine the pressure unfolding of proteins. Proc Natl Acad Sci U S A (2012) 1.52
Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides. Nucleic Acids Res (2006) 1.47
Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein. Proteins (2010) 1.45
NF-kappa B-mediated MyoD decay during muscle wasting requires nitric oxide synthase mRNA stabilization, HuR protein, and nitric oxide release. Mol Cell Biol (2005) 1.43
MicroRNA modulation of RNA-binding protein regulatory elements. RNA Biol (2006) 1.35
Differential phosphorylation and subcellular localization of La RNPs associated with precursor tRNAs and translation-related mRNAs. Mol Cell (2003) 1.25
Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms. J Mol Biol (2010) 1.23
Resistance to RevM10 inhibition reflects a conformational switch in the HIV-1 Rev response element. Proc Natl Acad Sci U S A (2008) 1.22
Conversions of formaldehyde-modified 2'-deoxyadenosine 5'-monophosphate in conditions modeling formalin-fixed tissue dehydration. J Histochem Cytochem (2005) 1.21
Simulations of the pressure and temperature unfolding of an alpha-helical peptide. Proc Natl Acad Sci U S A (2005) 1.21
Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer. Proteins (2005) 1.20
A boost for the emerging field of RNA nanotechnology. ACS Nano (2011) 1.17
Direct mass spectrometric determination of the stoichiometry and binding affinity of the complexes between nucleocapsid protein and RNA stem-loop hairpins of the HIV-1 Psi-recognition element. Biochemistry (2003) 1.15
Determination of thermodynamics and kinetics of RNA reactions by force. Q Rev Biophys (2006) 1.13
Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation. Anal Chem (2004) 1.10
MS3D structural elucidation of the HIV-1 packaging signal. Proc Natl Acad Sci U S A (2008) 1.10
Prospective type 1 and type 2 disulfides of Keap1 protein. Chem Res Toxicol (2008) 1.09
Fundamental molecular mechanism for the cellular uptake of guanidinium-rich molecules. J Am Chem Soc (2014) 1.08
Asymmetric segregation of the double-stranded RNA binding protein Staufen2 during mammalian neural stem cell divisions promotes lineage progression. Cell Stem Cell (2012) 1.06
Dissecting the protein-RNA and RNA-RNA interactions in the nucleocapsid-mediated dimerization and isomerization of HIV-1 stemloop 1. J Mol Biol (2006) 1.03
Untying the FIV frameshifting pseudoknot structure by MS3D. J Mol Biol (2005) 1.03
RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol (2011) 1.01
Cell penetrating peptides: how do they do it? J Biol Phys (2008) 1.01
Size and sequence and the volume change of protein folding. J Am Chem Soc (2011) 1.00
MHC-peptide binding is assisted by bound water molecules. J Mol Biol (2004) 0.98
Direct probing of RNA structures and RNA-protein interactions in the HIV-1 packaging signal by chemical modification and electrospray ionization fourier transform mass spectrometry. J Mol Biol (2003) 0.98
Understanding the isomerization of the HIV-1 dimerization initiation domain by the nucleocapsid protein. J Mol Biol (2007) 0.97
SHAMS: combining chemical modification of RNA with mass spectrometry to examine polypurine tract-containing RNA/DNA hybrids. RNA (2009) 0.95
Gene expression analysis of messenger RNP complexes. Methods Mol Biol (2004) 0.95
Mirror images as naturally competing conformations in protein folding. J Phys Chem B (2012) 0.94
Structural probing of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands. Nucleic Acids Res (2008) 0.94
Inhibitory effects of archetypical nucleic acid ligands on the interactions of HIV-1 nucleocapsid protein with elements of Psi-RNA. Nucleic Acids Res (2006) 0.93
Molecular mechanism for the preferential exclusion of TMAO from protein surfaces. J Phys Chem B (2012) 0.93
The collaboratory for MS3D: a new cyberinfrastructure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches. J Proteome Res (2008) 0.93
An alpha-helical peptide in AOT micelles prefers to be localized at the water/headgroup interface. Biophys J (2009) 0.91
Toward building a database of bifunctional probes for the MS3D investigation of nucleic acids structures. J Am Soc Mass Spectrom (2006) 0.91
Mapping noncovalent ligand binding to stemloop domains of the HIV-1 packaging signal by tandem mass spectrometry. J Am Soc Mass Spectrom (2006) 0.91
Folding a protein in the computer: reality or hope? Structure (2005) 0.89
Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain. J Mol Biol (2010) 0.89
Nested Arg-specific bifunctional crosslinkers for MS-based structural analysis of proteins and protein assemblies. Anal Chim Acta (2008) 0.89
Effect of internal cavities on folding rates and routes revealed by real-time pressure-jump NMR spectroscopy. J Am Chem Soc (2013) 0.89
Folding of a highly conserved diverging turn motif from the SH3 domain. Biophys J (2003) 0.87
Atmospheric pressure MALDI-FTMS of normal and chemically modified RNA. J Am Soc Mass Spectrom (2005) 0.87
Clerocidin alkylates DNA through its epoxide function: evidence for a fine tuned mechanism of action. Nucleic Acids Res (2003) 0.86
Remodeling of the folding free energy landscape of staphylococcal nuclease by cavity-creating mutations. Biochemistry (2012) 0.86
The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations. J Mol Biol (2010) 0.86
Protein conformational space populated in solution probed with aromatic residual dipolar (13) C-(1) H couplings. Chembiochem (2013) 0.86
Toward multiplexing the application of solvent accessibility probes for the investigation of RNA three-dimensional structures by electrospray ionization-Fourier transform mass spectrometry. Anal Biochem (2004) 0.86
Noncovalent probes for the investigation of structure and dynamics of protein-nucleic acid assemblies: the case of NC-mediated dimerization of genomic RNA in HIV-1. Biopolymers (2009) 0.86
Combining temperature and force to study folding of an RNA hairpin. Phys Chem Chem Phys (2013) 0.85
Structure-based design of a heptavalent anthrax toxin inhibitor. Biomacromolecules (2011) 0.85
Identification of a novel non-carbohydrate molecule that binds to the ribosomal A-site RNA. Bioorg Med Chem Lett (2004) 0.85
RIP: an mRNA localization technique. Methods Mol Biol (2011) 0.85
Protonation/deprotonation effects on the stability of the Trp-cage miniprotein. Phys Chem Chem Phys (2011) 0.84
Discriminating early stage A{beta}42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study. Proc Natl Acad Sci U S A (2010) 0.84
Bioinformatic tools for studying post-transcriptional gene regulation : The UAlbany TUTR collection and other informatic resources. Methods Mol Biol (2008) 0.84
Like polarity ion/ion reactions enable the investigation of specific metal interactions in nucleic acids and their noncovalent assemblies. J Am Chem Soc (2008) 0.83
Correction of apparent finite size effects in the area per lipid of lipid membranes simulations. J Chem Phys (2006) 0.82
Alkylation of nucleic acids by the antitumor agent COMC. Org Lett (2002) 0.82
Concerted bis-alkylating reactivity of clerocidin towards unpaired cytosine residues in DNA. Nucleic Acids Res (2004) 0.82
Probing anomalous structural features in polypurine tract-containing RNA-DNA hybrids with neomycin B. Biochemistry (2009) 0.82
Simulation studies of protein folding/unfolding equilibrium under polar and nonpolar confinement. J Am Chem Soc (2011) 0.81
Involvement of human intracisternal A-type retroviral particles in autoimmunity. Microsc Res Tech (2005) 0.81
Rapid purification of RNA secondary structures. Nucleic Acids Res (2003) 0.81
Experimental test of the thermodynamic model of protein cooperativity using temperature-induced unfolding of a Ubq-UIM fusion protein. Biochemistry (2010) 0.81
Direct infusion analysis of nucleotide mixtures of very similar or identical elemental composition. J Mass Spectrom (2013) 0.81
Effects of common buffer systems on drug activity: the case of clerocidin. Chem Res Toxicol (2004) 0.80
Informatic resources for identifying and annotating structural RNA motifs. Mol Biotechnol (2008) 0.80
Measuring the binding stoichiometry of HIV-1 Gag to very-low-density oligonucleotide surfaces using surface plasmon resonance spectroscopy. J Biomol Tech (2007) 0.79
Dutasteride monotherapy in men with serologic relapse following radical therapy for adenocarcinoma of the prostate: a pilot study. Urol Oncol (2010) 0.79
Backtracking due to residual structure in the unfolded state changes the folding of the third fibronectin type III domain from tenascin-C. J Phys Chem B (2013) 0.78
Mass spectrometric investigation of protein alkylation by the RNA footprinting probe kethoxal. J Mass Spectrom (2005) 0.78
RIP-CHIP in drug development. Methods Mol Biol (2010) 0.77
Pressure effects on the ensemble dynamics of ubiquitin inspected with molecular dynamics simulations and isotropic reorientational eigenmode dynamics. Biophys J (2008) 0.77
Neurodevelopmental disorders: Signalling pathways of fragile X syndrome. Nature (2012) 0.77
Current-controlled nanospray ionization mass spectrometry. J Am Soc Mass Spectrom (2009) 0.77
Atmospheric pressure MALDI-fourier transform mass spectrometry. Anal Chem (2004) 0.77
Structural, energetic, and dynamic responses of the native state ensemble of staphylococcal nuclease to cavity-creating mutations. Proteins (2013) 0.77
Transgenic expression of ZBP1 in neurons suppresses cocaine-associated conditioning. Learn Mem (2012) 0.77
Ribonomic and short hairpin RNA gene silencing methods to explore functional gene programs associated with tumor growth arrest. Methods Mol Biol (2007) 0.76
Web-based tools for studying RNA structure and function. Methods Mol Biol (2011) 0.76
Perturbation of local solvent structure by a small dication: a theoretical study on structural, vibrational, and reactive properties of beryllium ion in water. J Phys Chem B (2008) 0.76
102 Force and temperature dependent folding of a 2-base-pair RNA kissing complex. J Biomol Struct Dyn (2015) 0.75
103 Structural polymorphism of CAG RNA repeats investigated by single-molecule mechanical unfolding. J Biomol Struct Dyn (2015) 0.75
Erratum: Profiling ribonucleotide modifications at full-transcriptome level: a step toward MS-based epitranscriptomics. RNA (2015) 0.75
Dissecting reactivity of clerocidin toward common buffer systems by means of selected drug analogues. Chem Res Toxicol (2005) 0.75