Drug Designing Methodologies

The fundamental problem in the design of computational drugs is to accurately estimate the affinity of ligand-receptor binding. Historically, this deficiency combined with complexity, resources and time requirements have hampered the utility of drug design based on structure.

However, Moore's Law, along with recent advances in GPU-driven computing, have made it possible to obtain accurate results within reasonable time frames.

These calculations are performed alchemically using molecular dynamics to adequately sample an adequate thermodynamic path and intermediate states. The energies measured during the alchemical transformation are then used to computationally calculate the ligand-receptor binding affinity by a series of published techniques, including:

  • Thermodynamic integration

  • Weighted histogram analysis method

  • Bennett acceptance ratio

  • Linear interaction energy

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