Free Energy Correction to Rigid Body Docking: Application to the Colicin E7 and Im7 Complex

  • Authors:

  • Sangwook Wu;Vasu Chandrasekaran;Lee G. Pedersen

  • Affiliations:

  • Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290;Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290;Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290 and Laboratory of Structural Biology, NIEHS, RTP, NC 27709-12233

  • Venue:
  • ICCS 2009 Proceedings of the 9th International Conference on Computational Science
  • Year:
  • 2009

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Abstract

We performed a 2-dimensional free energy calculation in the conformational space composed of two structures, best RMSD (Root Mean Square Distance) and the worst RMSD structures using ZDOCK on the Colicin E7 (protein) and Im7 (Inhibitor) complex. The lowest free energy minimum structure is compared to the X-ray crystal structure and the best RMSD docking structure. The free energy correction for the best RMSD structure shows an alternative in the prediction of a flexible loop position, which could not describe rigid body docking.