Scoring functions in protein folding and design.
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.
Dima
R I
RI
Department of Physics and Center for Materials Physics, The Pennsylvania State University, University Park 16802, USA. dima@ipst.umd.edu
Banavar
J R
JR
Maritan
A
A
D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding