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Fast protein folding in the hydrophobichydrophilic model within threeeights of optimal
 1ZDD 34 1045 4.0 2.703 3.12 1Q2N 0.66 0.61 1VII 36 14280 7.4 3.047 12.59 1UNC 0.74 0.70 1EOM 37 36000 3.4 3.093 17.41 1I5H 0.47 0.49 1EDO 46 36000 7.2 3.656 11.54 1NBL 0.55 0.56 2IGD 61 174960 11.5 7.469 8.01 1MVK 0.79 0.74 1YPA 64 420840 9.4 6.687 0.34 2
, 1996
"... We present performanceguaranteed approximation algorithms for the protein folding problem in the hydrophobichydrophilic model (Dill, 1985). Our algorithms are the first approximation algorithms in the literature with guaranteed performance for this model (Dill, 1994). The hydrophobichydrophilic m ..."
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Cited by 73 (4 self)
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We present performanceguaranteed approximation algorithms for the protein folding problem in the hydrophobichydrophilic model (Dill, 1985). Our algorithms are the first approximation algorithms in the literature with guaranteed performance for this model (Dill, 1994). The hydrophobichydrophilic
Fast Protein Folding in the Hydrophobichydrophilic Model Within Threeeights of Optimal Abstract
"... We present performanceguaranteed approximation algorithms for the protein folding problem in the hydrophobichydrophilic model, Dill (1985). To our knowledge, our algorithms arethe first approximation algorithms inthe literature with guaranteed performance for this model, Dill (1994). The hydrophobi ..."
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). The hydrophobichydrophilic model abstracts the dominant force of protein folding: the hydrophobic interaction. The protein is modeled as a chain of amino acids of length n which are of two types: H (hydrophobic, i.e., nonpolar) and P (hydrophilic, i.e., polar). Although this model is a simplification of more
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
Fast Parallel Algorithms for ShortRange Molecular Dynamics
 JOURNAL OF COMPUTATIONAL PHYSICS
, 1995
"... Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dyn ..."
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Cited by 622 (6 self)
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Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular
FAST VOLUME RENDERING USING A SHEARWARP FACTORIZATION OF THE VIEWING TRANSFORMATION
, 1995
"... Volume rendering is a technique for visualizing 3D arrays of sampled data. It has applications in areas such as medical imaging and scientific visualization, but its use has been limited by its high computational expense. Early implementations of volume rendering used bruteforce techniques that req ..."
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Cited by 541 (2 self)
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that require on the order of 100 seconds to render typical data sets on a workstation. Algorithms with optimizations that exploit coherence in the data have reduced rendering times to the range of ten seconds but are still not fast enough for interactive visualization applications. In this thesis we present a
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
Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. sect
 A
, 1991
"... Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallographic refinement and result in an incorrect structure. The normally quoted crystallographic residual is often a poor description for the q ..."
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Cited by 1016 (9 self)
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for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the modelbuilding process, quantify the goodness of fit of the model on a perresidue basis and locate possible errors in peptide and sidechain conformations.
Protein Secondary Structure Prediction . . .
 JO MOL B/O/. (1999) 292, 195202 .GG
, 1999
"... ..."
Graphical models, exponential families, and variational inference
, 2008
"... The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building largescale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fiel ..."
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Cited by 800 (26 self)
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The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building largescale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical
Dynamic topic models
 In ICML
, 2006
"... Scientists need new tools to explore and browse large collections of scholarly literature. Thanks to organizations such as JSTOR, which scan and index the original bound archives of many journals, modern scientists can search digital libraries spanning hundreds of years. A scientist, suddenly ..."
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Cited by 656 (28 self)
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Scientists need new tools to explore and browse large collections of scholarly literature. Thanks to organizations such as JSTOR, which scan and index the original bound archives of many journals, modern scientists can search digital libraries spanning hundreds of years. A scientist, suddenly
Results 1  10
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