• Publications
  • Influence
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization. Thermodynamic parameters for the stabilities of secondary structure motifsExpand
  • 3,548
  • 377
  • PDF
Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide
This article is about the current status of the mfold package for RNA and DNA secondary structure prediction using nearest neighbor thermodynamic rules. Expand
  • 1,226
  • 133
  • PDF
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy incrementsExpand
  • 1,189
  • 128
  • PDF
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs.
Improved thermodynamic parameters for prediction of RNA duplex formation are derived from optical melting studies of 90 oligoribonucleotide duplexes containing only Watson-Crick base pairs. To testExpand
  • 974
  • 44
  • PDF
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.
An RNA model system consisting of an oligomer binding to a 4-nt overhang at the 5' end of a hairpin stem provides thermodynamic parameters for helix-helix interfaces. In a sequence-dependent manner,Expand
  • 473
  • 36
  • PDF
Improved free-energy parameters for predictions of RNA duplex stability.
Thermodynamic parameters for prediction of RNA duplex stability are reported. One parameter for duplex initiation and 10 parameters for helix propagation are derived from enthalpy and free-energyExpand
  • 1,162
  • 34
  • PDF
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.
With the rapid increase in the size of the genome sequence database, computational analysis of RNA will become increasingly important in revealing structure-function relationships and potential drugExpand
  • 402
  • 34
Improved predictions of secondary structures for RNA.
The accuracy of computer predictions of RNA secondary structure from sequence data and free energy parameters has been increased to roughly 70%. Performance is judged by comparison with structuresExpand
  • 724
  • 32
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
The Nearest Neighbor Database (NNDB, http://rna.urmc.rochester.edu/NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities. Expand
  • 333
  • 31
  • PDF
Predicting thermodynamic properties of RNA.
Publisher Summary This chapter discusses the thermodynamic properties of RNA and explores the rules governing the folding of biological molecules into their three-dimensional structures. RNA is anExpand
  • 297
  • 25