Browsing Faculty of Arts and Sciences by Author "Dokholyan, Nikolay V."

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    • Expanding protein universe and its origin from the biological Big Bang 

      Dokholyan, Nikolay V.; Shakhnovich, Boris; Shakhnovich, Eugene I. (National Academy of Sciences, 2002)
      The bottom-up approach to understanding the evolution of organisms is by studying molecular evolution. With the large number of protein structures identified in the past decades, we have discovered peculiar patterns that ...

    • Imprint of evolution on protein structures 

      Tiana, Guido; Shakhnovich, Boris E.; Dokholyan, Nikolay V.; Shakhnovich, Eugene I. (National Academy of Sciences, 2004)
      We attempt to understand the evolutionary origin of protein folds by simulating their divergent evolution with a three-dimensional lattice model. Starting from an initial seed lattice structure, evolution of model proteins ...

    • Topological determinants of protein folding 

      Dokholyan, Nikolay V.; Li, Lewyn; Ding, Feng; Shakhnovich, Eugene I. (National Academy of Sciences, 2002)
      The folding of many small proteins is kinetically a two-state process that represents overcoming the major free-energy barrier. A kinetic characteristic of a conformation, its probability to descend to the native state ...

    • Using protein design for homology detection and active site searches 

      Pei, Jimin; Dokholyan, Nikolay V.; Shakhnovich, Eugene I.; Grishin, Nick V. (National Academy of Sciences, 2003)
      We describe a method of designing artificial sequences that resemble naturally occurring sequences in terms of their compatibility with a template structure and its functional constraints. The design procedure is a Monte ...