Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

Adaptation in natural and artificial systems

1975 • 36,178 citations

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

1981 • 3,596 citations

Light-Directed, Spatially Addressable Parallel Chemical Synthesis

1991 • 2,692 citations

Fast folding and comparison of RNA secondary structures

1994 • 2,262 citations

On Finding All Suboptimal Foldings of an RNA Molecule

1989 • 2,019 citations

Compilation of tRNA sequences and sequences of tRNA genes

2004 • 1,921 citations

Improved free-energy parameters for predictions of RNA duplex stability.

1986 • 1,472 citations

Intramolecular Reaction in Polycondensations. I. The Theory of Linear Systems

1950 • 1,354 citations

The equilibrium partition function and base pair binding probabilities for RNA secondary structure

1990 • 1,321 citations

Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing

1996 • 1,240 citations

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

1990 • 1,239 citations

Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson−Crick Base Pairs

1998 • 1,111 citations

Genetic Algorithms: Principles of Natural Selection Applied to Computation

1993 • 856 citations

Improved predictions of secondary structures for RNA.

1989 • 822 citations

Compilation of tRNA sequences and sequences of tRNA genes

1998 • 776 citations

Comparative and functional anatomy of group II catalytic introns — a review

1989 • 768 citations

Stability of ribonucleic acid double-stranded helices

1974 • 760 citations

Probing the structure of RNAs in solution

1987 • 721 citations

Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids

1983 • 643 citations

Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994

1994 • 533 citations

Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops".

1990 • 527 citations

Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.

1994 • 474 citations

A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993

1993 • 448 citations

The ribonuclease P database

1998 • 429 citations

Metals, Motifs, and Recognition in the Crystal Structure of a 5S rRNA Domain

1997 • 392 citations

Structure of an unusually stable RNA hairpin

1991 • 368 citations

CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes.

1988 • 357 citations

Frequent use of the same tertiary motif by self-folding RNAs.

1995 • 354 citations

[11] Predicting thermodynamic properties of RNA

1995 • 345 citations

The Computer Simulation of RNA Folding Pathways Using a Genetic Algorithm

1995 • 323 citations

Molecular Modeling of Nucleic Acids

1997 • 308 citations

Investigation of the Structural Basis for Thermodynamic Stabilities of Tandem GU Mismatches: Solution Structure of (rGAG<u>GU</u>CUC)₂ by Two-Dimensional NMR and Simulated Annealing^,

1996 • 295 citations

New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme

1996 • 291 citations

A thermodynamic study of unusually stable RNA and DNA hairpins

1991 • 288 citations

The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA

1974 • 287 citations

Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix

1994 • 276 citations

GAAA Tetraloop and Conserved Bulge Stabilize Tertiary Structure of a Group I Intron Domain

1994 • 246 citations

Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops

1992 • 241 citations

Involvement of a GNRA tetraloop in long-range RNA tertiary interactions

1994 • 241 citations

Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis

1998 • 234 citations

Major Groove Accessibility of RNA

1993 • 202 citations

Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips

1998 • 197 citations

Characterization of RNA hairpin loop stability

1988 • 197 citations

An APL-programmed genetic algorithm for the prediction of RNA secondary structure

1995 • 194 citations

[16] Enzymatic approaches to probing of RNA secondary and tertiary structure

1989 • 192 citations

Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing — a review

1984 • 190 citations

Using reliability information to annotate RNA secondary structures

1998 • 184 citations

Comprehensive Comparison of Structural Characteristics in Eukaryotic Cytoplasmic Large Subunit (23 S-like) Ribosomal RNA

1996 • 169 citations

Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure

1993 • 162 citations

4 Probing RNA Structure, Function, and History by Comparative Analysis

1993 • 160 citations

Phylogenetic analysis of tmRNA secondary structure.

1996 • 155 citations

Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides

1990 • 152 citations

Solution Structure of the CUUG Hairpin Loop: A Novel RNA Tetraloop Motif

1995 • 149 citations

Stabilities of consecutive A.cntdot.C, C.cntdot.C, G.cntdot.G, U.cntdot.C, and U.cntdot.U mismatches in RNA internal loops: evidence for stable hydrogen-bonded U.cntdot.U and C.cntdot.C+ pairs

1991 • 136 citations

Probing the structure of the Escherichia coli 10Sa RNA (tmRNA).

1997 • 136 citations

Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: an empirical estimate of the energetics of hydrogen bonds in nucleic acids

1986 • 125 citations

Assessing the reliability of RNA folding using statistical mechanics

1997 • 118 citations

A Periodic Table of Tandem Mismatches in RNA

1995 • 116 citations

A comparative database of group I intron structures

1994 • 114 citations

Free energy of imperfect nucleic acid helices

1972 • 111 citations

Solution structure of a GAAA tetraloop receptor RNA

1997 • 109 citations

Effects of 3' dangling end stacking on the stability of GGCC and CCGG double helixes

1983 • 108 citations

Nearest-neighbor parameters for G.cntdot.U mismatches: 5'GU3'/3'UG5' is destabilizing in the contexts CGUG/GUGC, UGUA/AUGU, and AGUU/UUGA but stabilizing in GGUC/CUGG

1991 • 108 citations

[18] Phylogenetic comparative analysis of RNA secondary structure

1989 • 105 citations

Thermodynamics of RNA Folding in a Conserved Ribosomal RNA Domain

1994 • 103 citations

‘Well-determined’ regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA

1995 • 103 citations

Monitoring of the Cooperative Unfolding of the sunY Group I Intron of Bacteriophage T4

1993 • 101 citations

The Signal Recognition Particle Database (SRPDB)

1999 • 99 citations

Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops

1991 • 95 citations

Energetics of internal GU mismatches in ribooligonucleotide helixes

1986 • 94 citations

Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element.

1997 • 89 citations

Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops

1991 • 88 citations

Free energy contributions of G.cntdot.U and other terminal mismatches to helix stability

1986 • 84 citations

Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces

1994 • 82 citations

Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by site-specific photoaffinity crosslinking.

1997 • 81 citations

RNA hairpin loop stability depends on closing base pair

1993 • 75 citations

The Stability and Structure of Tandem GA Mismatches in RNA Depend on Closing Base Pairs

1994 • 74 citations

Thermodynamics of Nonsymmetric Tandem Mismatches Adjacent to G·C Base Pairs in RNA

1997 • 73 citations

A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides

1994 • 70 citations

Thermodynamic Prediction of Conserved Secondary Structure: Application to the RRE Element of HIV, the tRNA-like Element of CMV and the mRNA of Prion Protein

1996 • 68 citations

Comparative structural analysis of nuclear RNase P RNAs from yeast

1993 • 66 citations

Thermodynamics of Coaxially Stacked Helixes with GA and CC Mismatches

1996 • 55 citations

Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide

1989 • 54 citations

Thermodynamic Analysis of an RNA Combinatorial Library Contained in a Short Hairpin

1998 • 52 citations

Stability of RNA Hairpins Closed by Wobble Base Pairs

1998 • 50 citations

The development of microfabricated arrays for DNA sequencing and analysis

1996 • 49 citations

An Interactive Framework for RNA Secondary Structure Prediction with a Dynamical Treatment of Constraints

1995 • 48 citations

Isoalloxazine derivatives promote photocleavage of natural RNAs at G.U base pairs embedded within helices

1997 • 48 citations

Investigation of the Structural Basis for Thermodynamic Stabilities of Tandem GU Wobble Pairs: NMR Structures of (rGGA<u>GU</u>UCC)₂ and (rGGA<u>UG</u>UCC)₂^,

1997 • 47 citations

Improved Parameters for the Prediction of RNA Hairpin Stability

1997 • 44 citations

Flavin-Dependent Photocleavage of RNA at G·U Base Pairs

1997 • 44 citations

Thermal unfolding of yeast glycine transfer RNA

1976 • 44 citations

Purine–purine mismatches in RNA helices: evidence for protonated G·A pairs and next-nearest neighbor effects

1995 • 40 citations

Structure-Sensitive RNA Footprinting of Yeast Nuclear Ribonuclease P

1994 • 39 citations

5S rRNA Data Bank

1998 • 39 citations

Thermodynamics of RNA hairpins containing single internal mismatches

1999 • 38 citations

An Updated Recursive Algorithm for RNA Secondary Structure Prediction with Improved Thermodynamic Parameters

1997 • 35 citations

Improved free energies for G · C base-pairs

1985 • 35 citations

G·A and U·U Mismatches Can Stabilize RNA Internal Loops of Three Nucleotides

1996 • 34 citations

The Signal Recognition Particle Database (SRPDB)

1998 • 34 citations

Kinetic and Secondary Structure Analysis of Naegleria andersoni GIR1, a Group I Ribozyme Whose Putative Biological Function Is Site-Specific Hydrolysis

1997 • 24 citations

Structural analyses of E.coli 5S RNA fragments, their associates and complexes with proteins L18 and L25

1982 • 21 citations

Secondary structure of a 345-base RNA fragment covering the S8/S15 protein binding domain of Escherichia coli 16 S ribosomal RNA

1985 • 21 citations

The Relative Stabilities of Base Pair Stacking Interactions and Single Mismatches in Long RNA Measured by Temperature Gradient Gel Electrophoresis

1997 • 21 citations