Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting.

ABSTRACT:

Motivation

A major limitation in modeling protein interactions is the difficulty of assessing the over-fitting of the training set. Recently, an experimentally based approach that integrates crystallographic information of C2H2 zinc finger-DNA complexes with binding data from 11 mutants, 7 from EGR finger I, was used to define an improved interaction code (no optimization). Here, we present a novel mixed integer programming (MIP)-based method that transforms this type of data into an optimized code, demonstrating both the advantages of the mathematical formulation to minimize over- and under-fitting and the robustness of the underlying physical parameters mapped by the code.

Results

Based on the structural models of feasible interaction networks for 35 mutants of EGR-DNA com

SUBMITTER: Temiz NA 

PROVIDER: S-EPMC2815656 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature