Focused grid-based resampling for protein docking and mapping
Artem B. Mamonov, Mohammad Moghadasi, Hanieh Mirzaei, Shahrooz Zarbafian, Laurie E. Grove, Tanggis Bohnuud, Pirooz Vakili, Ioannis Ch. Paschalidis, Sandor Vajda and Dima Kozakov
Article first published online: 2 FEB 2016 | DOI: 10.1002/jcc.24273
The fast Fourier transform (FFT) algorithm enables extremely fast evaluation of energy functions, and hence has been used with great success for protein-protein docking and for the characterization of the binding properties of proteins by docking small probe molecules. While both applications of FFT involve global systematic sampling, the same algorithm can also be used to refine the results by focused resampling on the regions of interest using finer grids or by retaining more structures.