Abstract
Ligand protein docking simulations play a fundamental role in understanding molecular recognition. Herein we introduce the NRGsuite, a PyMOL plugin that permits the detection of surface cavities in proteins, their refinements, calculation of volume and use, individually or jointly, as target binding-sites for docking simulations with FlexAID. The NRGsuite offers the users control over a large number of important parameters in docking simulations including the assignment of flexible side-chains and definition of geometric constraints. Furthermore, the NRGsuite permits the visualization of the docking simulation in real time. The NRGsuite give access to powerful docking simulations that can be used in structure-guided drug design as well as an educational tool. The NRGsuite is implemented in Python and C/C++ with an easy to use package installer. The NRGsuite is available for Windows, Linux and MacOS.Availability and implementation: http://bcb.med.usherbrooke.ca/flexaid.Contact: rafael.najmanovich@usherbroke.caSupplementary information: Supplementary data are available at Bioinformatics online.
Highlights
Docking simulations can be used to understand the specificity and selectivity of ligands as well as guide in the identification and design of inhibitors
Two PyMOL plugins exist for docking simulations (Lill and Danielson, 2011; Seeliger and de Groot, 2010), both use AutoDock Vina and require additional software compilation/installation
In this work we present the NRGsuite, an open-source and self-contained precompiled PyMOL plugin focused on the prediction of binding-poses with docking simulations
Summary
Docking simulations can be used to understand the specificity and selectivity of ligands as well as guide in the identification and design of inhibitors. Two PyMOL plugins exist for docking simulations (Lill and Danielson, 2011; Seeliger and de Groot, 2010), both use AutoDock Vina and require additional software compilation/installation. The latter permits docking with SLIDE (Zavodszky et al, 2002) but requires an AMBER license. In this work we present the NRGsuite, an open-source and self-contained precompiled PyMOL plugin (for PyMOL versions 1.2 and above) focused on the prediction of binding-poses with docking simulations. Project-oriented environment making structure-guided drug design accessible to non-experts
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
