Evaluation of comparative protein modeling by M<scp>ODELLER</scp>

TLDR

The study evaluates 3D comparative models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin generated by MODELLER. MODELLER, a comparative protein modeling program that satisfies spatial restraints, was used to calculate the models. The MODELLER-generated models exhibit good stereochemistry and are comparable to crystal structures, with errors mainly in poorly aligned or dissimilar regions such as exposed loops and insertions, and when a template shares >40 % sequence identity, the models achieve ~90 % main‑chain accuracy with an RMSD of ~1 Å, comparable to NMR‑X‑ray differences. © 1995 Wiley‑Liss, Inc.

Abstract

Abstract We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin that were calculated by M ODELLER , a program for comparative protein modeling by satisfaction of spatial restraints. The models have good stereochemistry and are at least as similar to the crystallographic structures as the closest template structures. The largest errors occur in the regions that were not aligned correctly or where the template structures are not similar to the correct structure. These regions correspond predominantly to exposed loops, insertions of any length, and non‐conserved side chains. When a template structure with more than 40% sequence identity to the target protein is available, the model is likely to have about 90% of the mainchain atoms modeled with an rms deviation from the X‐ray structure of ≈ 1 Å, in large part because the templates are likely to be that similar to the X‐ray structure of the target. This rms deviation is comparable to the overall differences between refined NMR and X‐ray crystallography structures of the same protein. © 1995 Wiley‐Liss, Inc.