Paper Citing NAMD - Abstract
Minh, David D. L.
Implicit ligand theory: Rigorous binding free energies and thermodynamic expectations from molecular docking
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 104106, SEP 14 2012
A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor configurations only need to be sampled once, facilitating the use of binding free energy calculations in virtual screening. Demonstrative calculations on a host-guest system yield good agreement with previous free energy calculations and isothermal titration calorimetry measurements. Implicit ligand theory provides guidance on how to improve existing molecular docking algorithms and insight into the concepts of induced fit and conformational selection in noncovalent macromolecular recognition. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4751284]
