Published in RNA on May 02, 2008
Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci U S A (2008) 5.44
Atomic accuracy in predicting and designing noncanonical RNA structure. Nat Methods (2010) 3.07
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA (2009) 2.63
Advances in RNA structure analysis by chemical probing. Curr Opin Struct Biol (2010) 2.24
iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics (2008) 2.03
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 1.88
New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA (2009) 1.78
On the significance of an RNA tertiary structure prediction. RNA (2010) 1.61
Developing three-dimensional models of putative-folding intermediates of the HDV ribozyme. Structure (2010) 1.49
Discrete RNA libraries from pseudo-torsional space. J Mol Biol (2012) 1.46
Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites. PLoS One (2015) 1.42
Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J Am Chem Soc (2009) 1.33
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. RNA (2015) 1.30
Turning limited experimental information into 3D models of RNA. RNA (2010) 1.27
Physics-based de novo prediction of RNA 3D structures. J Phys Chem B (2011) 1.21
Three-dimensional RNA structure refinement by hydroxyl radical probing. Nat Methods (2012) 1.20
Accurate and efficient reconstruction of deep phylogenies from structured RNAs. Nucleic Acids Res (2009) 1.19
RNA and protein 3D structure modeling: similarities and differences. J Mol Model (2011) 1.19
Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling. Nucleic Acids Res (2009) 1.18
A boost for the emerging field of RNA nanotechnology. ACS Nano (2011) 1.17
Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures. Proc Natl Acad Sci U S A (2009) 1.16
Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain. Biochemistry (2010) 1.13
Single-molecule correlated chemical probing of RNA. Proc Natl Acad Sci U S A (2014) 1.10
In silico selection of RNA aptamers. Nucleic Acids Res (2009) 1.09
Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models. Bioinformatics (2009) 1.06
Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. Curr Opin Struct Biol (2011) 1.04
Predicting loop-helix tertiary structural contacts in RNA pseudoknots. RNA (2010) 1.02
Vfold: a web server for RNA structure and folding thermodynamics prediction. PLoS One (2014) 1.02
The power of coarse graining in biomolecular simulations. Wiley Interdiscip Rev Comput Mol Sci (2014) 1.00
PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy. Proteins (2010) 0.99
Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant. Nucleic Acids Res (2011) 0.99
RNA structure determination using SAXS data. J Phys Chem B (2010) 0.99
Clustering to identify RNA conformations constrained by secondary structure. Proc Natl Acad Sci U S A (2011) 0.98
Nonhierarchical ribonucleoprotein assembly suggests a strain-propagation model for protein-facilitated RNA folding. Biochemistry (2010) 0.98
Modeling nucleic acids. Curr Opin Struct Biol (2012) 0.98
Coarse-grained model for simulation of RNA three-dimensional structures. J Phys Chem B (2010) 0.98
RNA Bricks--a database of RNA 3D motifs and their interactions. Nucleic Acids Res (2013) 0.98
Predicting and modeling RNA architecture. Cold Spring Harb Perspect 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
RNAlyzer--novel approach for quality analysis of RNA structural models. Nucleic Acids Res (2013) 0.95
Computational analysis of RNA structures with chemical probing data. Methods (2015) 0.93
The low-resolution solution structure of Vibrio cholerae Hfq in complex with Qrr1 sRNA. Nucleic Acids Res (2012) 0.93
Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints. J Comput Chem (2011) 0.93
The Mrs1 splicing factor binds the bI3 group I intron at each of two tetraloop-receptor motifs. PLoS One (2010) 0.93
Structural characterization of naturally occurring RNA single mismatches. Nucleic Acids Res (2010) 0.92
Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal. RNA (2011) 0.88
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev (2014) 0.88
RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information. Nucleic Acids Res (2015) 0.87
Regulatory RNAs in brain function and disorders. Brain Res (2010) 0.87
Determining RNA three-dimensional structures using low-resolution data. J Struct Biol (2012) 0.87
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction. Nucleic Acids Res (2015) 0.86
The role of nucleobase interactions in RNA structure and dynamics. Nucleic Acids Res (2014) 0.86
New models of Tetrahymena telomerase RNA from experimentally derived constraints and modeling. J Am Chem Soc (2012) 0.86
Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics. J Chem Theory Comput (2015) 0.85
Kinetics of tRNA folding monitored by aminoacylation. RNA (2012) 0.84
MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery. Int J Mol Sci (2015) 0.83
In vitro selection of RNA aptamers that inhibit the activity of type A botulinum neurotoxin. Biochem Biophys Res Commun (2010) 0.83
Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity. Phys Chem Chem Phys (2010) 0.83
iFoldRNA v2: folding RNA with constraints. Bioinformatics (2015) 0.83
Computational modeling of RNA 3D structures, with the aid of experimental restraints. RNA Biol (2014) 0.82
Physics-based RNA structure prediction. Biophys Rep (2015) 0.81
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions. J Mol Model (2014) 0.81
Steric exclusion and constraint satisfaction in multi-scale coarse-grained simulations. Comput Biol Chem (2016) 0.81
Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure. F1000 Biol Rep (2009) 0.81
Computational Prediction of RNA-Binding Proteins and Binding Sites. Int J Mol Sci (2015) 0.81
A conditional random fields method for RNA sequence-structure relationship modeling and conformation sampling. Bioinformatics (2011) 0.81
Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments. Nucleic Acids Res (2015) 0.80
A didactic model of macromolecular crowding effects on protein folding. PLoS One (2010) 0.80
On docking, scoring and assessing protein-DNA complexes in a rigid-body framework. PLoS One (2012) 0.80
Coarse-grained prediction of RNA loop structures. PLoS One (2012) 0.80
Improved prediction of RNA tertiary structure with insights into native state dynamics. RNA (2012) 0.79
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA (2017) 0.79
Exploring RNA conformational space under sparse distance restraints. Sci Rep (2017) 0.78
Many-body effect in ion binding to RNA. J Chem Phys (2014) 0.78
SimRNAweb: a web server for RNA 3D structure modeling with optional restraints. Nucleic Acids Res (2016) 0.78
Predicting RNA 3D structure using a coarse-grain helix-centered model. RNA (2015) 0.78
A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures. BMC Bioinformatics (2014) 0.77
RNA tertiary structure analysis by 2'-hydroxyl molecular interference. Biochemistry (2014) 0.77
Structure Prediction: New Insights into Decrypting Long Noncoding RNAs. Int J Mol Sci (2016) 0.77
Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A{middle dot}A base pairing and a putative structure of the coralyne-induced homo-adenine duplex. Nucleic Acids Res (2009) 0.77
Thermodynamics and kinetics of the hairpin ribozyme from atomistic folding/unfolding simulations. J Mol Biol (2011) 0.76
Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions. Biophys J (2015) 0.76
Applications of Discrete Molecular Dynamics in biology and medicine. Curr Opin Struct Biol (2015) 0.76
Coarse-graining RNA nanostructures for molecular dynamics simulations. Phys Biol (2010) 0.75
Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction. Nucleic Acids Mol Biol (2012) 0.75
Screening and Identifying a Novel ssDNA Aptamer against Alpha-fetoprotein Using CE-SELEX. Sci Rep (2015) 0.75
Computational identification of RNA functional determinants by three-dimensional quantitative structure-activity relationships. Nucleic Acids Res (2014) 0.75
Martini Coarse-Grained Force Field: Extension to RNA. Biophys J (2017) 0.75
What Can Human-Guided Simulations Bring to RNA Folding? Biophys J (2017) 0.75
De novo tertiary structure prediction using RNA123--benchmarking and application to Macugen. J Mol Model (2014) 0.75
Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. Biophys J (2017) 0.75
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48
Vienna RNA secondary structure server. Nucleic Acids Res (2003) 19.69
Non-coding RNA genes and the modern RNA world. Nat Rev Genet (2001) 9.06
How does a protein fold? Nature (1994) 7.55
A dynamic programming algorithm for RNA structure prediction including pseudoknots. J Mol Biol (1999) 6.19
How RNA folds. J Mol Biol (1999) 6.14
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc (2006) 6.14
RNA backbone is rotameric. Proc Natl Acad Sci U S A (2003) 5.93
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model (2004) 5.50
Automated de novo prediction of native-like RNA tertiary structures. Proc Natl Acad Sci U S A (2007) 3.87
Discrete molecular dynamics studies of the folding of a protein-like model. Fold Des (1998) 2.96
RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts. J Am Chem Soc (2005) 2.92
The combination of symbolic and numerical computation for three-dimensional modeling of RNA. Science (1991) 2.66
Pseudoknots: RNA structures with diverse functions. PLoS Biol (2005) 2.60
Bridging the gap in RNA structure prediction. Curr Opin Struct Biol (2007) 2.41
Single-molecule RNA science. Annu Rev Biophys Biomol Struct (2005) 1.93
Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Res (2006) 1.75
Revolutions in RNA secondary structure prediction. J Mol Biol (2006) 1.74
Multiscale modeling of nucleosome dynamics. Biophys J (2006) 1.63
Ribozyme structures and mechanisms. Annu Rev Biophys Biomol Struct (2001) 1.62
NMR structure of a classical pseudoknot: interplay of single- and double-stranded RNA. Science (1998) 1.61
How do RNA folding algorithms work? Nat Biotechnol (2004) 1.56
Mechanism for the alpha-helix to beta-hairpin transition. Proteins (2003) 1.51
Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J Mol Biol (1994) 1.48
Simple but predictive protein models. Trends Biotechnol (2005) 1.39
Does native state topology determine the RNA folding mechanism? J Mol Biol (2004) 1.30
Reproducing the three-dimensional structure of a tRNA molecule from structural constraints. Proc Natl Acad Sci U S A (1993) 1.29
Quantifying the energetic interplay of RNA tertiary and secondary structure interactions. RNA (1999) 1.27
Thermodynamics of folding a pseudoknotted mRNA fragment. J Mol Biol (1994) 1.19
Protein folding: then and now. Arch Biochem Biophys (2007) 1.18
iFold: a platform for interactive folding simulations of proteins. Bioinformatics (2006) 1.15
New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate. Structure (2004) 1.11
The principles of guiding by RNA: chimeric RNA-protein enzymes. Nat Rev Genet (2006) 1.08
Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function. Proc Natl Acad Sci U S A (2008) 3.08
Eris: an automated estimator of protein stability. Nat Methods (2007) 2.78
Engineered allosteric activation of kinases in living cells. Nat Biotechnol (2010) 2.44
Emergence of protein fold families through rational design. PLoS Comput Biol (2006) 2.35
Ab initio folding of proteins with all-atom discrete molecular dynamics. Structure (2008) 2.22
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics (2008) 2.03
RNA visualization in live bacterial cells using fluorescent protein complementation. Nat Methods (2007) 1.92
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 1.88
Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol (2003) 1.80
Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets. J Am Chem Soc (2002) 1.68
Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J Mol Biol (2002) 1.66
Modeling backbone flexibility improves protein stability estimation. Structure (2007) 1.65
Automated minimization of steric clashes in protein structures. Proteins (2011) 1.64
Multiscale modeling of nucleosome dynamics. Biophys J (2006) 1.63
Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating. J Biol Chem (2008) 1.62
On the significance of an RNA tertiary structure prediction. RNA (2010) 1.61
Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J (2002) 1.55
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
Mechanism for the alpha-helix to beta-hairpin transition. Proteins (2003) 1.51
Computational design of a PAK1 binding protein. J Mol Biol (2010) 1.51
Minihepcidins are rationally designed small peptides that mimic hepcidin activity in mice and may be useful for the treatment of iron overload. J Clin Invest (2011) 1.49
The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis. Proc Natl Acad Sci U S A (2004) 1.46
Modifications of superoxide dismutase (SOD1) in human erythrocytes: a possible role in amyotrophic lateral sclerosis. J Biol Chem (2009) 1.46
Can contact potentials reliably predict stability of proteins? J Mol Biol (2004) 1.44
Simple but predictive protein models. Trends Biotechnol (2005) 1.39
MedusaScore: an accurate force field-based scoring function for virtual drug screening. J Chem Inf Model (2008) 1.37
Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J Am Chem Soc (2009) 1.33
Regulatory insertion removal restores maturation, stability and function of DeltaF508 CFTR. J Mol Biol (2010) 1.31
GC/AT-content spikes as genomic punctuation marks. Proc Natl Acad Sci U S A (2004) 1.30
Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. Biophys J (2004) 1.29
Fast complementation of split fluorescent protein triggered by DNA hybridization. Proc Natl Acad Sci U S A (2006) 1.26
Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants. Proc Natl Acad Sci U S A (2006) 1.25
Imprint of evolution on protein structures. Proc Natl Acad Sci U S A (2004) 1.24
Predictions of CCR1 chemokine receptor structure and BX 471 antagonist binding followed by experimental validation. J Biol Chem (2006) 1.24
Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation. Proc Natl Acad Sci U S A (2008) 1.23
Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP. J Am Chem Soc (2010) 1.23
The path of DNA in the kinetochore. Curr Biol (2006) 1.22
Rapid flexible docking using a stochastic rotamer library of ligands. J Chem Inf Model (2010) 1.21
Three-dimensional RNA structure refinement by hydroxyl radical probing. Nat Methods (2012) 1.20
Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. J Mol Biol (2005) 1.18
Allosteric modulation balances thermodynamic stability and restores function of ΔF508 CFTR. J Mol Biol (2012) 1.18
Protein folding: then and now. Arch Biochem Biophys (2007) 1.18
Polyglutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences. PLoS Comput Biol (2010) 1.17
Molecular origin of polyglutamine aggregation in neurodegenerative diseases. PLoS Comput Biol (2005) 1.17
Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis. J Mol Biol (2003) 1.17
BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics. Mol Cell Proteomics (2008) 1.17
Correctors of ΔF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein. FASEB J (2012) 1.17
Principles for understanding the accuracy of SHAPE-directed RNA structure modeling. Biochemistry (2013) 1.16
iFold: a platform for interactive folding simulations of proteins. Bioinformatics (2006) 1.15
Topological determinants of protein domain swapping. Structure (2006) 1.15
Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. J Phys Chem B (2012) 1.14
Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain. Biochemistry (2010) 1.13
Deciphering protein dynamics from NMR data using explicit structure sampling and selection. Biophys J (2007) 1.13
Active nuclear receptors exhibit highly correlated AF-2 domain motions. PLoS Comput Biol (2008) 1.12
Selective reciprocity in antimicrobial activity versus cytotoxicity of hBD-2 and crotamine. Proc Natl Acad Sci U S A (2009) 1.11
New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate. Structure (2004) 1.11
The coordinated evolution of yeast proteins is constrained by functional modularity. Trends Genet (2006) 1.10
Regulation of the epithelial Na+ channel and airway surface liquid volume by serine proteases. Pflugers Arch (2010) 1.08
Diminished self-chaperoning activity of the DeltaF508 mutant of CFTR results in protein misfolding. PLoS Comput Biol (2008) 1.08
Rational design of a ligand-controlled protein conformational switch. Proc Natl Acad Sci U S A (2013) 1.08
Fidelity of the protein structure reconstruction from inter-residue proximity constraints. J Phys Chem B (2007) 1.06
The complex molecular biology of amyotrophic lateral sclerosis (ALS). Prog Mol Biol Transl Sci (2012) 1.05
Fast screening of protein surfaces using geometric invariant fingerprints. Proc Natl Acad Sci U S A (2009) 1.05
Structural and dynamic determinants of protein-peptide recognition. Structure (2011) 1.04
Harnessing a physiologic mechanism for siRNA delivery with mimetic lipoprotein particles. Mol Ther (2012) 1.04
Structural determinants of skeletal muscle ryanodine receptor gating. J Biol Chem (2013) 1.03
Spatiotemporal patterns and transcription kinetics of induced RNA in single bacterial cells. Proc Natl Acad Sci U S A (2009) 1.03
Insights into allosteric control of vinculin function from its large scale conformational dynamics. J Biol Chem (2006) 1.03
Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR. J Mol Biol (2008) 1.01
A single disulfide bond differentiates aggregation pathways of beta2-microglobulin. J Mol Biol (2005) 1.01
Glutathionylation at Cys-111 induces dissociation of wild type and FALS mutant SOD1 dimers. Biochemistry (2011) 1.00
Identification of a consensus motif in substrates bound by a Type I Hsp40. Proc Natl Acad Sci U S A (2009) 1.00
Scaling behavior and structure of denatured proteins. Structure (2005) 1.00
Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm. Mol Biol Evol (2008) 0.99
Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. J Mol Biol (2002) 0.99
Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant. Nucleic Acids Res (2011) 0.99
Critical structural and functional roles for the N-terminal insertion sequence in surfactant protein B analogs. PLoS One (2010) 0.99
Using protein design for homology detection and active site searches. Proc Natl Acad Sci U S A (2003) 0.99
Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics. J Mol Biol (2007) 0.99
A structural model reveals energy transduction in dynein. Proc Natl Acad Sci U S A (2006) 0.98
FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis. Amyloid (2006) 0.98
Structural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase. J Mol Biol (2011) 0.97
Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers. PLoS Comput Biol (2008) 0.97
Local unfolding of Cu, Zn superoxide dismutase monomer determines the morphology of fibrillar aggregates. J Mol Biol (2011) 0.96
Antimicrobial peptide RP-1 structure and interactions with anionic versus zwitterionic micelles. Biopolymers (2009) 0.96
Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation. Proteins (2005) 0.96
Direct observation of protein folding, aggregation, and a prion-like conformational conversion. J Biol Chem (2005) 0.96
The length dependence of the polyQ-mediated protein aggregation. J Biol Chem (2007) 0.95
A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1). PLoS Comput Biol (2009) 0.94
Gaia: automated quality assessment of protein structure models. Bioinformatics (2011) 0.94
Kinetic models for the coordinated stepping of cytoplasmic dynein. J Chem Phys (2009) 0.94
Knowledge-based design of a biosensor to quantify localized ERK activation in living cells. Chem Biol (2013) 0.93
Rolling-circle amplification under topological constraints. Nucleic Acids Res (2002) 0.93
Protein evolution within a structural space. Biophys J (2003) 0.92
Retrocyclin RC-101 overcomes cationic mutations on the heptad repeat 2 region of HIV-1 gp41. FEBS J (2007) 0.91