Software

Funnel-Metadynamics Advanced Protocol (FMAP)

Funnel-Metadynamics Advanced Protocol (FMAP) is a flexible and user-friendly graphical user interface (GUI)-based protocol to perform Funnel-Metadynamics, a binding free-energy method that employs a funnel-shape restraint potential to reveal the ligand binding mode and accurately calculate the absolute ligand–protein binding free energy. FMAP guides the user through all phases of the free-energy calculation process, from preparation of the input files, to production simulation, to analysis of the results. FMAP delivers the ligand binding mode and the absolute protein–ligand binding free energy as outputs. Alternative binding modes and the role of waters are also elucidated, providing a detailed description of the ligand binding mechanism.

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plumed.mp4

Want to try it? Funnel-Metadynamics has been implemented in the latest version of Plumed-2. Here you will be able to download it. Instead, the GUI are available at the following link.

Drug Discovery Tool (DDT)

Drug Discovery Tool (DDT) is an intuitive graphics user interface able to provide structural data and physico-chemical information on the ligand/protein interaction. DDT is designed as a plugin for the Visual Molecular Dynamics (VMD) software and is able to manage a large number of ligand/protein complexes obtained from AutoDock4 (AD4) docking calculations and MD simulations. DDT delivers four main outcomes:

ligands ranking based on an energy score;
ligand ranking based on a ligands’ conformation cluster analysis;
identification of the aminoacids forming the most occurrent interactions with the ligands;
plot of the ligands’ center-of-mass coordinates in the Cartesian space.

Want to try it? DDT can be downloaded from the following link.