ct8b01208_si_001.pdf (1.37 MB)
Predicting Protein Dimer Structures Using MELD × MD
journal contribution
posted on 2019-03-25, 00:00 authored by Emiliano Brini, Dima Kozakov, Ken A. DillIt
is challenging to predict the docked conformations of two proteins.
Current methods are susceptible to errors from treating proteins as
rigid bodies and from an inability to compute relative Boltzmann populations
of different docked conformations. Here, we show that by using the
ClusPro server as a front end to generate possible protein–protein
contacts, and using Modeling Employing Limited Data (MELD) accelerated
molecular dynamics (MELD × MD) as a back end for atomistic simulations,
we can find 16/20 native dimer structures of small proteins as those
having the lowest free energy, starting from good–bound–backbone
structures. We show that atomistic MD free energies can be used to
identify native protein dimer structures.