posted on 2021-09-14, 12:10authored byStamatia Zavitsanou, Alexandros Tsengenes, Michail Papadourakis, Giorgio Amendola, Alexios Chatzigoulas, Dimitris Dellis, Sandro Cosconati, Zoe Cournia
Relative binding free energy calculations
in drug design are becoming
a useful tool in facilitating lead binding affinity optimization in
a cost- and time-efficient manner. However, they have been limited
by technical challenges such as the manual creation of large numbers
of input files to set up, run, and analyze free energy simulations.
In this Application Note, we describe FEPrepare, a novel web-based
tool, which automates the setup procedure for relative binding FEP
calculations for the dual-topology scheme of NAMD, one of the major
MD engines, using OPLS-AA force field topology and parameter files.
FEPrepare provides the user with all necessary files needed to run
a FEP/MD simulation with NAMD. FEPrepare can be accessed and used
at https://feprepare.vi-seem.eu/.