3697115
doi
10.5281/zenodo.3697115
oai:zenodo.org:3697115
Limongelli, Vittorio
Università della Svizzera Italiana
FMAP data files
Raniolo, Stefano
Università della Svizzera Italiana
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
ligand binding mode
ligand binding free energy
molecular docking
molecular dynamics
funnel-metadynamics
enhanced sampling
free-energy calculations
<p>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. </p>
<p>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.</p>
<p>This package contains inputs and outputs files of FMAP produced for the paradigmatic benzamidine-trypsin system.</p>
We would like to acknowledge the support of the Italian MIUR-PRIN 2017 (project id 2017FJZZRC) and the Swiss National Supercomputing Centre (CSCS) [project ID u8].
Zenodo
2020-03-04
info:eu-repo/semantics/other
3697114
1.00
award_title=Extensive computer simulations investigate TPP1-TERT protein-protein interaction; award_number=200021_163281; funder_id=00yjd3n13; funder_name=Swiss National Science Foundation;
1583349653.349473
117955936
md5:f0d93fd3144838ac49c37b85136e6ff4
https://zenodo.org/records/3697115/files/FMAP_data.tar.gz
public
10.5281/zenodo.3697114
isVersionOf
doi