Constrained geometric simulation of diffusive motion in proteins

Phys Biol. 2005 Nov 9;2(4):S127-36. doi: 10.1088/1478-3975/2/4/S07.


We describe a new computational method, FRODA (framework rigidity optimized dynamic algorithm), for exploring the internal mobility of proteins. The rigid regions in the protein are first determined, and then replaced by ghost templates which are used to guide the movements of the atoms in the protein. Using random moves, the available conformational phase space of a 100 residue protein can be well explored in approximately 10-100 min of computer time using a single processor. All of the covalent, hydrophobic and hydrogen bond constraints are maintained, and van der Waals overlaps are avoided, throughout the simulation. We illustrate the results of a FRODA simulation on barnase, and show that good agreement is obtained with nuclear magnetic resonance experiments. We additionally show how FRODA can be used to find a pathway from one conformation to another. This directed dynamics is illustrated with the protein dihydrofolate reductase.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Bacillus / metabolism
  • Biophysics / methods*
  • Computational Biology / methods*
  • Computer Simulation
  • Diffusion
  • Hydrogen Bonding
  • Magnetic Resonance Spectroscopy
  • Models, Chemical
  • Models, Molecular
  • Models, Theoretical
  • Molecular Conformation
  • Polymers / chemistry
  • Protein Conformation
  • Proteins / chemistry*


  • Polymers
  • Proteins