Calculating nucleic acid secondary structure (Q47853339)

6 February 2018

title

Calculating nucleic acid secondary structure (English)

1 reference

6 February 2018

author name string

Zuker M

series ordinal

1

1 reference

6 February 2018

publication date

1 June 2000

1 reference

6 February 2018

Current Opinion in Structural Biology

published in

1 reference

6 February 2018

volume

10

1 reference

6 February 2018

issue

3

1 reference

6 February 2018

page(s)

303-310

1 reference

6 February 2018

SECONDARY STRUCTURE IN RIBONUCLEIC ACIDS.

cites work

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Some molecular details of the secondary structure of ribonucleic acid

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

RNA secondary structures and their prediction

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Compilation of tRNA sequences and sequences of tRNA genes

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Multistranded DNA structures

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Computer prediction of RNA structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

A dynamic programming algorithm for finding alternative RNA secondary structures

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Sequence alignments in the neighborhood of the optimum with general application to dynamic programming

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

On finding all suboptimal foldings of an RNA molecule

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Conformational Transitions in Viroids and Virusoids: Comparison of Results from Energy Minimization Algorithm and from Experimental Data

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Fast folding and comparison of RNA secondary structures

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Prediction of common folding structures of homologous RNAs

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Stochastic context-free grammars for tRNA modeling

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

RNA sequence analysis using covariance models

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Predicting DNA duplex stability from the base sequence

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Recursion relation generation of probability profiles for specific-sequence macromolecules with long-range correlations.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Theory of DNA melting curves

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Improved nearest-neighbor parameters for predicting DNA duplex stability

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Thermodynamics and NMR of Internal G·T Mismatches in DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Nearest Neighbor Thermodynamic Parameters for Internal G·A Mismatches in DNA

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Thermodynamics of internal C.T mismatches in DNA.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Estimation of Secondary Structure in Ribonucleic Acids

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Free energy of imperfect nucleic acid helices. I. The bulge defect

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Free energy of imperfect nucleic acid helices. II. Small hairpin loops

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Improved Estimation of Secondary Structure in Ribonucleic Acids

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Stability of RNA hairpin loops: A6-Cm-U6

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Stability of ribonucleic acid double-stranded helices

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Globin mRNA Sequences: Analysis of Base Pairing and Evolutionary Implications

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Improved free-energy parameters for predictions of RNA duplex stability

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Improved parameters for prediction of RNA structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

RNA structure prediction

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

A periodic table of symmetric tandem mismatches in RNA.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Thermodynamics of single mismatches in RNA duplexes

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Thermodynamics of RNA hairpins containing single internal mismatches

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

G.A and U.U mismatches can stabilize RNA internal loops of three nucleotides

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

An approximation of loop free energy values of RNA H-pseudoknots

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Fast evaluation of internal loops in RNA secondary structure prediction.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

A dynamic programming algorithm for RNA structure prediction including pseudoknots

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Complete suboptimal folding of RNA and the stability of secondary structures.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

An RNA folding method capable of identifying pseudoknots and base triples

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

A method for assessing the statistical significance of RNA folding.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Structural analysis by energy dot plot of a large mRNA.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

"Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Base pairing probabilities in a complete HIV-1 RNA.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Energy directed folding of RNA sequences.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Assessing the reliability of RNA folding using statistical mechanics

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

The European large subunit ribosomal RNA database

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

A comparative database of group I intron structures

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

The European small subunit ribosomal RNA database

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

1 reference

7 January 2021

The Ribonuclease P Database

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

The database of the smallest known auto-replicable RNA species: viroids and viroid-like RNAs

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

5S ribosomal RNA database Y2K

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

1 reference

7 January 2021

tmRDB (tmRNA database)

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

A functional ribosomal RNA tertiary structure involves a base triple interaction

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Finding the most significant common sequence and structure motifs in a set of RNA sequences

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

RAGA: RNA sequence alignment by genetic algorithm

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Prediction of common secondary structures of RNAs: a genetic algorithm approach

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Automatic detection of conserved RNA structure elements in complete RNA virus genomes

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Conserved features of Y RNAs revealed by automated phylogenetic secondary structure analysis

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

RNA secondary structure prediction based on free energy and phylogenetic analysis

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

RNA secondary structure prediction using stochastic context-free grammars and evolutionary history

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Generating non-overlapping displays of nucleic acid secondary structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

A vector-based method for drawing RNA secondary structure.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

ESSA: an integrated and interactive computer tool for analysing RNA secondary structure

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Stem Trace: an interactive visual tool for comparative RNA structure analysis

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Sequence logos: a new way to display consensus sequences

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Using reliability information to annotate RNA secondary structures

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

RNA movies: visualizing RNA secondary structure spaces

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Exposing the kinetic traps in RNA folding

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

The folding of large RNAs studied by hybridization to arrays of complementary oligonucleotides

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Prediction of sequentially optimal RNA secondary structures

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

The computer simulation of RNA folding pathways using a genetic algorithm.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Kinetics of conformational fluctuations in DNA hairpin-loops

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

A computational screen for methylation guide snoRNAs in yeast

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

Collection of mRNA-like non-coding RNAs

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

A bayesian statistical algorithm for RNA secondary structure prediction

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2800%2900088-9

7 January 2021

10.1016/S0959-440X(00)00088-9

Identifiers

DOI

1 reference

6 February 2018

1 reference

6 February 2018