Evaluation of comparative protein modeling by MODELLER

Proteins. 1995 Nov;23(3):318-26. doi: 10.1002/prot.340230306.


We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin that were calculated by MODELLER, 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 approximately 1 A, 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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Computer Communication Networks
  • Computer Graphics
  • Computer Simulation
  • Crystallography, X-Ray
  • Databases, Factual
  • Eosinophil-Derived Neurotoxin
  • Humans
  • Magnetic Resonance Spectroscopy
  • Mice
  • Models, Molecular*
  • Molecular Sequence Data
  • Neurotoxins / chemistry*
  • Nucleoside-Diphosphate Kinase / chemistry*
  • Protein Conformation*
  • Protein Structure, Tertiary
  • Receptors, Retinoic Acid / chemistry*
  • Ribonucleases*
  • Sequence Alignment
  • Software*
  • Templates, Genetic


  • Neurotoxins
  • Receptors, Retinoic Acid
  • retinoic acid binding protein I, cellular
  • Nucleoside-Diphosphate Kinase
  • Eosinophil-Derived Neurotoxin
  • Ribonucleases