Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. Journal Article uri icon



  • We present a technique for biomolecular free energy calculations that exploits highly parallelized sampling to significantly reduce the time to results. The technique combines free energies for multiple, nonoverlapping configurational macrostates and is naturally suited to distributed computing. We describe a methodology that uses this technique with docking, molecular dynamics, and free energy perturbation to compute absolute free energies of binding quickly compared to previous methods. The method does not require a priori knowledge of the binding pose as long as the docking technique used can generate reasonable binding modes. We demonstrate the method on the protein FKBP12 and eight of its inhibitors.

publication date

  • August 28, 2006

has subject area

has restriction

  • closed

Date in CU Experts

  • September 4, 2015 2:15 AM

Full Author List

  • Jayachandran G; Shirts MR; Park S; Pande VS

author count

  • 4

Other Profiles

International Standard Serial Number (ISSN)

  • 0021-9606

Additional Document Info

start page

  • 084901


  • 125


  • 8