Comparative Protein Structure Prediction

Abstract Functional characterization of a protein sequence is one of the most frequent problems in biology. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3‐D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3‐D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target‐template alignment, model building, and model evaluation. Comparative modeling remains the only method to reliably predict the 3‐D structure of a protein with an accuracy comparable to a low‐resolution experimentally determined structure. This overview unit describes generic considerations for all four steps of comparative modeling, typical modeling errors, and applications of comparative protein structure models.