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1 results

  • Scoring functions in protein folding and design

  • RUXANDRA I. DIMA, JAYANTH R. BANAVAR, AMOS MARITAN
  • Journal:
    Protein Science / Volume 9 / Issue 4 / April 2000
    Published online by Cambridge University Press:
    01 April 2000, pp. 812-819
    Print publication:
    April 2000

  • We present an analysis of the assumptions behind some of the most commonly used methods for evaluating the goodness of the fit between a sequence and a structure. Our studies on a lattice model show that methods based on statistical considerations are easy to use and can capture some of the features of protein-like sequences and their corresponding native states, but unfortunately are incapable of recognizing, with certainty, the native-like conformation of a sequence among a set of decoys. Meanwhile, an optimization method, entailing the determination of the parameters of an effective free energy of interaction, is much more reliable in recognizing the native state of a sequence. However, the statistical method is shown to perform quite well in tests of protein design.