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14,547
The Vienna RNA Secondary Structure Server
- Nucleic Acids Res
, 2003
"... The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently o#ers prediction of secondary structure from a single sequence, prediction of the consensus secondary ..."
Abstract
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Cited by 611 (23 self)
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The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently o#ers prediction of secondary structure from a single sequence, prediction of the consensus
Protein Secondary Structure Prediction . . .
- JO MOL B/O/. (1999) 292, 195-202 .GG
, 1999
"... ..."
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
, 1983
"... For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-r ..."
Abstract
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Cited by 2096 (5 self)
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For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern
Fast Folding and Comparison of RNA Secondary Structures (The Vienna RNA Package)
"... Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and bas ..."
Abstract
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Cited by 809 (117 self)
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Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions
PF: Secondary structure prediction for aligned RNA sequences.
- J Mol Biol
, 2002
"... Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA sequences taking into account both thermodynamic stability and sequence covariation. Comparison with phy ..."
Abstract
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Cited by 331 (43 self)
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Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA sequences taking into account both thermodynamic stability and sequence covariation. Comparison
Knowledge-based protein secondary structure assignment
- Proteins
, 1995
"... ABSTRACT We have developed an auto-matic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone tor-sional angle information. Parameters of the pattern recognition procedure were optimiz ..."
Abstract
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Cited by 324 (2 self)
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ABSTRACT We have developed an auto-matic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone tor-sional angle information. Parameters of the pattern recognition procedure were
Predicting the secondary structure of globular proteins using neural networks models
- J. Molecular Biology
, 1988
"... We present a new method for predicting the secondary structure of globular proteins based on non-linear neural network models. Network models learn from existing protein structures how to predict the secondary structure of local sequences of amino acids. The average success rate of our method on a t ..."
Abstract
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Cited by 271 (2 self)
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We present a new method for predicting the secondary structure of globular proteins based on non-linear neural network models. Network models learn from existing protein structures how to predict the secondary structure of local sequences of amino acids. The average success rate of our method on a
Complete suboptimal folding of RNA and the stability of secondary structures
- BIOPOLYMERS 49:145–165
, 1999
"... An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm is particularly fast in the vicinity of the minimum free energy. This enables the efficient approximation of statistical quantities, s ..."
Abstract
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Cited by 215 (23 self)
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An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm is particularly fast in the vicinity of the minimum free energy. This enables the efficient approximation of statistical quantities
Local similarity in RNA secondary structures
, 2003
"... We present a systematic treatment of alignment distance and local similarity algorithms on trees and forests. We build upon the tree alignment algorithm for ordered trees given by Jiang et. al (1995) and extend it to calculate local forest alignments, which is essential for finding local similar reg ..."
Abstract
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Cited by 110 (4 self)
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regions in RNA secondary structures. The time complexity of our algorithm is O(|F1 | ·|F2 | ·deg(F1) · deg(F2) · (deg(F1) +deg(F2)) where |Fi | is the number of nodes in forest Fi and deg(Fi) is the degree of Fi. We provide carefully engineered dynamic programming implementations using dense, two
Results 1 - 10
of
14,547
