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    BMCBI
    2007
    216views more  BMCBI 2007»
    A replica exchange Monte Carlo algorithm for protein folding in the HP model
    13 years 10 months ago
    A replica exchange Monte Carlo algorithm for protein folding in the HP model
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    Background: The ab initio protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing an energy function; it is one of...
    Chris Thachuk, Alena Shmygelska, Holger H. Hoos
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    BMCBI
    2007
    115views more  BMCBI 2007»
    Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites
    13 years 10 months ago
    Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites
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    Background: We performed an exhaustive search for local structural similarities in an ensemble of non-redundant protein functional sites. With the purpose of finding new examples ...
    Gabriele Ausiello, Daniele Peluso, Allegra Via, Ma...
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    LPAR
    2005
    Springer
    107views Automated Reasoning» more  LPAR 2005»
    A New Constraint Solver for 3D Lattices and Its Application to the Protein Folding Problem
    14 years 3 months ago
    A New Constraint Solver for 3D Lattices and Its Application to the Protein Folding Problem
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    Abstract. The paper describes the formalization and implementation of an efficient constraint programming framework operating on 3D crystal lattices. The framework is motivated an...
    Alessandro Dal Palù, Agostino Dovier, Enric...
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    BMCBI
    2007
    135views more  BMCBI 2007»
    RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that un
    13 years 10 months ago
    RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that un
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    Background: Most single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in un...
    Dianhui Zhu, George E. Fox, Sugoto Chakravarty
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    BMCBI
    2002
    133views more  BMCBI 2002»
    Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model app
    13 years 10 months ago
    Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model app
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    Background: Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. The next step of such database studies should include ...
    Kevin Truong, Mitsuhiko Ikura
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