Drug Designing Methodologies
The fundamental problem in computational drug design is accurately estimating ligand-receptor binding affinity. Historically, this shortcoming combined with the complexity, resources, and time requirements has hampered the utility of structure-based drug design.
However, Moore’s Law coupled with recent developments in GPU (Graphics Processing Unit) driven computing has made it possible to achieve accurate results in reasonable time frames.
These calculations are performed chemically using molecular dynamics to adequately sample a suitable thermodynamic path and intermediate states. The measured energies during chemical transformation are then used to computationally estimate ligand-receptor binding affinity by a number of published techniques - including Thermodynamic integration