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Protein Science, Vol 9, Issue 4 812-819, Copyright © 2000 by The Protein Society

JOURNAL ARTICLE

Scoring functions in protein folding and design

RI Dima, JR Banavar and A Maritan
Department of Physics and Center for Materials Physics, The Pennsylvania State University, University Park 16802, USA. dima@ipst.umd.edu

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.
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 Proc. Natl. Acad. Sci. USAHome page
I. Chang, M. Cieplak, R. I. Dima, A. Maritan, and J. R. Banavar
Protein threading by learning
PNAS, November 15, 2001; (2001) 241133698.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
I. Chang, M. Cieplak, R. I. Dima, A. Maritan, and J. R. Banavar
Protein threading by learning
PNAS, December 4, 2001; 98(25): 14350 - 14355.
[Abstract] [Full Text] [PDF]


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