Dataset Open Access
FMAP data files
Raniolo, Stefano;
Limongelli, Vittorio
The accurate study of the binding mechanism of a ligand to its molecular target is fundamental to discover new possible drug targets. In order to do that, we can employ free-energy calculations due to their accuracy, although the lack in user-friendliness generally hampers their broad application.
In this regard, the Funnel-Metadynamics Advanced Protocol (FMAP) represents a flexible and user-friendly protocol to perform Funnel-Metadynamics, a binding free-energy method that employs a funnel-shape restraint potential to obtain the ligand binding mode and the accurate calculation of the absolute ligand/protein binding free energy. Through the use of graphical interfaces, FMAP is able to assist the user during all steps of the investigation, allowing to disclose the ligand binding mode and mechanism and accurately compute the absolute protein/ligand binding free energy.
This package contains inputs and outputs files of FMAP produced for the paradigmatic benzamidine-trypsin system.
| Name | Size | |
|---|---|---|
|
FMAP_data.tar.gz
md5:f0d93fd3144838ac49c37b85136e6ff4 |
118.0 MB | Download |
| All versions | This version | |
|---|---|---|
| Views | 787 | 787 |
| Downloads | 753 | 753 |
| Data volume | 88.8 GB | 88.8 GB |
| Unique views | 726 | 726 |
| Unique downloads | 421 | 421 |
- Publication date:
- March 4, 2020
- DOI:
-
- Keyword(s):
- ligand binding mode ligand binding free energy molecular docking molecular dynamics funnel-metadynamics enhanced sampling free-energy calculations
- Grants:
-
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung:
- Extensive computer simulations investigate TPP1-TERT protein-protein interaction (200021_163281)
- License (for files):
- Creative Commons Attribution 4.0 International