Using GIST and 3D-RISM approaches, Flare provides insights into binding pockets that you can exploit in your inhibitor strategy
Calculate optimal locations of water around your ligands
Design new ligands and understand their water interactions
Perfect protein electrostatic analysis by including stable waters in the calculations.
GIST uses the OpenMM dynamics engine running on GPUs to analyze water stability. It can be used both on empty and liganded proteins and in each case generates heat surface maps that highlight regions of high and low water stability.
GIST uses OpenMM running on GPUs to analyze water stability generating heat surface maps that highlight regions of high and low water stability.
3D-RISM analysis in Flare utilizes the advanced inter-molecular descriptions of the XED force field or of the AMBER GAFF force field to give you a water analysis you can trust. 3D-RISM will give results across the whole protein or can be used to place waters within the active site, with or without a ligand present.
3D-RISM analysis uses the advanced inter-molecular descriptions of the XED force field to give you a water analysis you can trust.
S. Ramsey, C. Nguyen, R. Salomon-Ferrer, R. C. Walker, M. K. Gilson, T. Kurtzman, Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST, J Comput. Chem. 2016, 37(21):2029-37
R. Skyner, J.L McDonagh, C.R. Groom, T. van Mourik, J. B. O. Mitchell, C. R. Groom, T. Van Mourik, A Review of Methods for the Calculation of Solution Free Energies and the Modelling of Systems in Solution, Phys. Chem. Chem. Phys. 2015, 17 (9), 6174
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