Improved protein structure selection using decoy-dependent discriminatory functions.

ABSTRACT:

Background

A key component in protein structure prediction is a scoring or discriminatory function that can distinguish near-native conformations from misfolded ones. Various types of scoring functions have been developed to accomplish this goal, but their performance is not adequate to solve the structure selection problem. In addition, there is poor correlation between the scores and the accuracy of the generated conformations.

Results

We present a simple and nonparametric formula to estimate the accuracy of predicted conformations (or decoys). This scoring function, called the density score function, evaluates decoy conformations by performing an all-against-all Calpha RMSD (Root Mean Square Deviation) calculation in a given decoy set. We tested the density score function

SUBMITTER: Wang K 

PROVIDER: S-EPMC449718 | biostudies-literature | 2004 Jun

REPOSITORIES: biostudies-literature