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Scoring functions in protein folding and design

Published online by Cambridge University Press:  01 April 2000

RUXANDRA I. DIMA ,
JAYANTH R. BANAVAR  and
AMOS MARITAN
RUXANDRA I. DIMA
Affiliation:
Department of Physics and Center for Materials Physics, 104 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802
JAYANTH R. BANAVAR
Affiliation:
Department of Physics and Center for Materials Physics, 104 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802
AMOS MARITAN
Affiliation:
International School for Advanced Studies (S.I.S.S.A.), Via Beirut 2-4, 34014 Trieste, INFM and the Abdus Salam International Center for Theoretical Physics, Trieste, Italy
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Abstract

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.

Keywords

energy-based approachMonte Carlo procedureperceptron optimization procedurestatistical approachthree-dimensional lattice model
Type
Research Article
Information
Protein Science , Volume 9 , Issue 4 , April 2000 , pp. 812 - 819
Copyright
© 2000 The Protein Society

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