Results 1 - 10 of 215

The RNA folding problem

by Peter B. Moore - In: The RNA World* 1999
"... Because the chemical and biological properties of many RNAs are deter-mined by their conformations, an RNA equivalent exists to the protein folding problem. The RNA folding problem has both a practical side and an academic side. If the practical problem were solved, it would be pos-sible to predict ..."
Abstract - Cited by 4 (0 self) - Add to MetaCart
Because the chemical and biological properties of many RNAs are deter-mined by their conformations, an RNA equivalent exists to the protein folding problem. The RNA folding problem has both a practical side and an academic side. If the practical problem were solved, it would be pos-sible to predict

RNA chaperones and the RNA folding problem

by Daniel Herschlag - J. Biol. Chem , 1995
"... Functional and structural inter-relationships of RNA and proteins in the execution and control of biological processes such as RNA processing, RNA splicing, and translation are increasingly apparent. In this minireview, I present an RNA chaperone hypothesis, which fosters the view that constraints i ..."
Abstract - Cited by 150 (6 self) - Add to MetaCart
imposed by fundamental problems in the folding of RNA have profoundly influenced the nature of RNA/protein interactions in biology. The origin of this view is outlined as follows. RNA has two fundamental folding problems: a tendency to fold into and become kinetically trapped in alternative conformations

Lynx: A Programmatic SAT Solver for the RNA-folding Problem

by Vijay Ganesh, Charles W. O’donnell, Mate Soos, Srinivas Devadas, Martin Rinard, O Solar-lezama
"... Abstract. This paper introduces Lynx, an incremental programmatic SAT solver that allows non-expert users to easily introduce domain-specific code into modern Conflict-driven Clause-learning (CDCL) SAT solvers, thus enabling users to control the behavior of the solver in ways not possible otherwise. ..."
Abstract - Cited by 1 (1 self) - Add to MetaCart
very effective strategy that addresses this need. We demonstrate the benefits of Lynx through a case-study from computational biology, namely, RNA secondary structure prediction. The constraints that make up this problem fall into two categories: structural constraints, which describe properties

Correspondence

by Martina Doetsch, Renée Schroeder, Boris Fürtig, B. Fürtig, Department Of Biochemistry, Molecular Cell Biology, Max F. Perutz , 2010
"... mode of binding; proteins that promote RNA folding; RNA chaperones; RNA folding problem; transient interactions ..."
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mode of binding; proteins that promote RNA folding; RNA chaperones; RNA folding problem; transient interactions

Fast Folding and Comparison of RNA Secondary Structures (The Vienna RNA Package)

by Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. Sebastian Bonhoeffer, Manfred Tacker, Peter Schuster
"... 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 - Cited by 809 (117 self) - Add to MetaCart
and base pairing probabilities. An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment. All computer codes are written in ANSI C. They include

Mfold web server for nucleic acid folding and hybridization prediction

by Michael Zuker - Nucleic Acids Res , 2003
"... The abbreviated name,‘mfold web server’,describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding ..."
Abstract - Cited by 1992 (0 self) - Add to MetaCart
The abbreviated name,‘mfold web server’,describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding

RNA Folding and Large N Matrix Theory

by Henri Orl, A. Zee , 2001
"... We formulate the RNA folding problem as an N × N matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is set up in such a way that the limit N → ∞ yields the so-called sec ..."
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We formulate the RNA folding problem as an N × N matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is set up in such a way that the limit N → ∞ yields the so

RNA folding and large N matrix theory

by unknown authors , 2001
"... We formulate the RNA folding problem as an N × N matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is set up in such a way that the limit N →∞yields the so-called second ..."
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We formulate the RNA folding problem as an N × N matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is set up in such a way that the limit N →∞yields the so

Simultaneous solution of the RNA folding, alignment, and protosequence problems

by David Sankoff - SIAM J. APPL. MATH , 1985
"... ..."
Abstract - Cited by 309 (1 self) - Add to MetaCart
Abstract not found

Linear models and empirical bayes methods for assessing differential expression in microarray experiments.

by Gordon K Smyth , Gordon K Smyth - Stat. Appl. Genet. Mol. Biol. , 2004
"... Abstract The problem of identifying differentially expressed genes in designed microarray experiments is considered. Lonnstedt and Speed (2002) derived an expression for the posterior odds of differential expression in a replicated two-color experiment using a simple hierarchical parametric model. ..."
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Abstract The problem of identifying differentially expressed genes in designed microarray experiments is considered. Lonnstedt and Speed (2002) derived an expression for the posterior odds of differential expression in a replicated two-color experiment using a simple hierarchical parametric model
Results 1 - 10 of 215