Significantly boost the predictivity of Free Energy Perturbation (FEP) calculations with Grand Canonical Nonequilibrium Candidate Monte Carlo (GCNCMC)

Protein-ligand binding predictions generated by FEP calculations help drug designers to improve the efficiency of their work, and reach an active compound more quickly, at a lower overall cost, by minimizing the number of compounds that require synthesis within the lab.

Grand Canonical Nonequilibrium Candidate Monte Carlo (GCNCMC) improves the accuracy of such simulations, by performing water insertions and deletions in a gradual, nonequilibrium fashion, to enhance the sampling of hydration patterns in the protein active site.

When used during the equilibrium stage of Flare™ FEP calculations, it can significantly boost the predictivity of the method, especially in protein-ligand complexes where the active site features difficult-to-hydrate pockets. Also applicable to Molecular Dynamics (MD) simulations, the method can help enhance the exploration of the conformational space of the bound ligand, meaning that fewer MD simulations need to be run to generate accurate results.

GCNCMC is now available within Flare, alongside a comprehensive portfolio of both ligand-based and structure-based drug design methods.

When recently interviewed by Lucy Lawrence, Senior Digital Content Producer at scientific news publication, Technology Networks, Cresset’s Head of Products, Giovanna Tedesco spoke around the benefits of using Flare to accelerate drug discovery projects, for the greatest chances of success.

The reason why chemists use Flare within both industry and academia is common for all users: finding new, better ligands, optimizing these ligands, and accelerating the time it takes to bring new drugs to the market

Giovanna Tedesco - Head of Products, Cresset

Flare receives bi-annual updates, as part of our ambitions to respond to customer feedback and desire to provide users with access to the very latest science and CADD methods. Within this ‘Teach me in 10’ video, which challenges scientists to present and summarize their products or research areas within 10 minutes or less, Giovanna took a deeper dive into GCNCMC, and some of the other newly added features, within the latest Flare Version 7 updates, which included:

  • Ensemble Covalent Docking
  • The new semi-empirical method for performing Quantum Mechanics calculations
  • Enhanced capabilities for building quantitative SAR models
  • Graphical User Interface (GUI) and usability improvements

Watch our episode via the below recording and gain a complete overview of Flare in just 10 minutes! 

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