Our Computational Tools
MD (Molecular Dynamics)
MD simulations allow us to observe and study the physical movements of atoms and molecules. In a typical MD simulation, all the atoms of the systems are represented, and the interaction between each pair of atoms is defined. During the simulations, the atom positions are updated using Newton's equation of motion. MD simulations can be used to determine macroscopic thermodynamic properties of the system. We commonly use the open-source python-based OpenMM software as our MD engine.
MELD (Modeling Employing Limited Data)
MELD is our tool to accelerate molecular dynamic simulations. It allows to focus the computational effort of our simulation around areas that agree with external information. MELD is abased on a Bayesian framework, that allows us to use sparse, ambiguous, and uncertain information coming from experiments, bioinformatics tools, and general knowledge about our systems.
SEA (Semi Explicit Assembly)
SEA is our tool to compute solvation free energies. SEA is fast and accurate. SEA accuracy comes from a rigorous treatment of the physics of water-solute interaction. SEA speed comes from the fact that most quantities that contribute to the calculation of a solvation free energy can be pre-computed, making run-time execution as fast as looking up numbers from a table.