The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

Chem Soc Rev. 2014 Jul 7;43(13):4871-93. doi: 10.1039/c4cs00048j. Epub 2014 Apr 23.

Abstract

The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.

Publication types

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

MeSH terms

  • Amyloid / chemistry*
  • DNA / chemistry*
  • Models, Molecular*
  • Proteins / chemistry*
  • RNA / chemistry*

Substances

  • Amyloid
  • Proteins
  • RNA
  • DNA