1. FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations
- Author
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Dimitris Dellis, Zoe Cournia, Sandro Cosconati, Giorgio Amendola, Stamatia Zavitsanou, Alexios Chatzigoulas, Michail Papadourakis, Alexandros Tsengenes, Zavitsanou, S., Tsengenes, A., Papadourakis, M., Amendola, G., Chatzigoulas, A., Dellis, D., Cosconati, S., and Cournia, Z.
- Subjects
Scheme (programming language) ,Binding free energy ,Computer science ,Entropy ,General Chemical Engineering ,Molecular Dynamics Simulation ,Library and Information Sciences ,01 natural sciences ,Force field (chemistry) ,Computational science ,Physical Phenomena ,Set (abstract data type) ,03 medical and health sciences ,0103 physical sciences ,Web application ,Topology (chemistry) ,030304 developmental biology ,computer.programming_language ,Internet ,0303 health sciences ,010304 chemical physics ,business.industry ,General Chemistry ,Computer Science Applications ,Thermodynamics ,business ,computer ,Energy (signal processing) - Abstract
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/.
- Published
- 2021
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