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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 ..."
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Cited by 812 (119 self)
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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
PROTEIN FOLDING THEORY: From Lattice to AllAtom Models
, 2001
"... Key Words nucleation, folding nucleus conservation, molecular dynamics, structure prediction, folding nucleus prediction n Abstract This review focuses on recent advances in understanding protein folding kinetics in the context of nucleation theory. We present basic concepts such as nucleation, fol ..."
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folding nucleus and analyze other aspects of folding kinetics. Finally, we briefly discuss successful allatom MonteCarlo simulations of protein folding and conclude with a brief outlook for the future.
MolProbity: allatom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35: W375–383
, 2007
"... and nucleic acids ..."
A simple method for displaying the hydropathic character of a protein
 Journal of Molecular Biology
, 1982
"... A computer program that progressively evaluates the hydrophilicity and hydrophobicity of a protein along its amino acid sequence has been devised. For this purpose, a hydropathy scale has been composed wherein the hydrophilic and hydrophobic properties of each of the 20 amino acid sidechains is tak ..."
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Cited by 2249 (2 self)
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A computer program that progressively evaluates the hydrophilicity and hydrophobicity of a protein along its amino acid sequence has been devised. For this purpose, a hydropathy scale has been composed wherein the hydrophilic and hydrophobic properties of each of the 20 amino acid side
Simulating Physics with Computers
 SIAM Journal on Computing
, 1982
"... A digital computer is generally believed to be an efficient universal computing device; that is, it is believed able to simulate any physical computing device with an increase in computation time of at most a polynomial factor. This may not be true when quantum mechanics is taken into consideration. ..."
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Cited by 601 (1 self)
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A digital computer is generally believed to be an efficient universal computing device; that is, it is believed able to simulate any physical computing device with an increase in computation time of at most a polynomial factor. This may not be true when quantum mechanics is taken into consideration
A survey of generalpurpose computation on graphics hardware
, 2007
"... The rapid increase in the performance of graphics hardware, coupled with recent improvements in its programmability, have made graphics hardware acompelling platform for computationally demanding tasks in awide variety of application domains. In this report, we describe, summarize, and analyze the l ..."
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Cited by 545 (18 self)
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The rapid increase in the performance of graphics hardware, coupled with recent improvements in its programmability, have made graphics hardware acompelling platform for computationally demanding tasks in awide variety of application domains. In this report, we describe, summarize, and analyze
Protein Secondary Structure Prediction . . .
 JO MOL B/O/. (1999) 292, 195202 .GG
, 1999
"... ..."
Dictionary of protein secondary structure: pattern recognition of hydrogenbonded and geometrical features
 Biopolymers
, 1983
"... structure ..."
The SWISSMODEL Workspace: A webbased environment for protein structure homology modelling
 BIOINFORMATICS
, 2005
"... Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental threedimensional structures are available. Building homology models requires specialized programs and uptodate sequence and structural databases. Integrating all re ..."
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Cited by 555 (5 self)
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Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental threedimensional structures are available. Building homology models requires specialized programs and uptodate sequence and structural databases. Integrating all
Primitives for the manipulation of general subdivisions and the computations of Voronoi diagrams
 ACM Tmns. Graph
, 1985
"... The following problem is discussed: Given n points in the plane (the sites) and an arbitrary query point 4, find the site that is closest to q. This problem can be solved by constructing the Voronoi diagram of the given sites and then locating the query point in one of its regions. Two algorithms ar ..."
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Cited by 543 (11 self)
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The following problem is discussed: Given n points in the plane (the sites) and an arbitrary query point 4, find the site that is closest to q. This problem can be solved by constructing the Voronoi diagram of the given sites and then locating the query point in one of its regions. Two algorithms are given, one that constructs the Voronoi diagram in O(n log n) time, and another that inserts a new site in O(n) time. Both are based on the use of the Voronoi dual, or Delaunay triangulation, and are simple enough to be of practical value. The simplicity of both algorithms can be attributed to the separation of the geometrical and topological aspects of the problem and to the use of two simple but powerful primitives, a geometric predicate and an operator for manipulating the topology of the diagram. The topology is represented by a new data structure for generalized diagrams, that is, embeddings of graphs in twodimensional manifolds. This structure represents simultaneously an embedding, its dual, and its mirror image. Furthermore, just two operators are sufficient for building and modifying arbitrary diagrams.
Results 1  10
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