Sequence Design in Coarse-Grained Protein Models
نویسندگان
چکیده
منابع مشابه
Sequence Design in Coarse-Grained Protein Models
Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is explored over and over again for different fixed sequences. In this paper we discuss an alternative Monte Carlo approach, multisequence design, where conformation and sequ...
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Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders are discussed. Similar patterns for non-randomness are found for real proteins. Dynamical parameter MC methods, such as the tempering and multisequence algorit...
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The aggregation of soluble proteins into fibrillar species is a complex process that spans many lengths and time scales, and that involves the formation of numerous on-pathway and off-pathway intermediate species. Despite this complexity, several elements underlying the aggregation process appear to be universal. The kinetics typically follows a nucleation-growth process, and proteins with very...
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BACKGROUND Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplishing this is a nested Monte Carlo where the conformation space is explored over and over again for different fixed sequences; this requires excessive computational demand. Several approximate attempts to remedy this situati...
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Rotamer libraries usually contain geometric information to trace an amino acid side chain, atom by atom, onto a protein backbone. These libraries have been widely used in protein design, structure refinement and prediction, homology modeling, and X-ray and NMR structure validation. However, they usually present too much information and are not always fully compatible with the coarse-grained mod...
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ژورنال
عنوان ژورنال: Progress of Theoretical Physics Supplement
سال: 2000
ISSN: 0375-9687
DOI: 10.1143/ptps.138.273