Coarse-grained model of proteins incorporating atomistic detail of the active site

Phys Rev Lett. 2005 Nov 18;95(21):218102. doi: 10.1103/PhysRevLett.95.218102. Epub 2005 Nov 16.


We present a novel approach to explore the conformational space of globular proteins near their native state. It combines the advantages of coarse-grained models with those of all-atoms simulations, required to treat molecular recognition processes. The comparison between calculated structural properties with those obtained with all-atoms molecular dynamics simulations establishes the accuracy of the model. Our method has the potential to be extended to molecular recognition processes in systems whose characteristic size and time scale prevent an analysis based on all-atoms molecular dynamics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amyloid Precursor Protein Secretases
  • Aspartic Acid Endopeptidases
  • Binding Sites
  • Computer Simulation
  • Endopeptidases / chemistry*
  • HIV Protease / chemistry*
  • Humans
  • Models, Molecular
  • Protein Conformation
  • Static Electricity
  • Stochastic Processes


  • Amyloid Precursor Protein Secretases
  • Endopeptidases
  • Aspartic Acid Endopeptidases
  • HIV Protease
  • BACE1 protein, human