The paper discusses a technique called Metadynamics which can be used to estimate the binding free energy, it mentions the equations and procedure for this technique as well as a case study.
It also describes pharmacophores obtained from molecular dynamics simulations, otherwise known as dynophores. Finally, A procedure to find a representative pharmacophore model from a MD simulation is explained.
Lupia, Antonio, Federica Moraca, Donatella Bagetta, Annalisa Maruca, Francesca Alessandra Ambrosio, Roberta Rocca, Raffaella Catalano, et al. “Computer-Based Techniques for Lead Identification and Optimization II: Advanced Search Methods.” Physical Sciences Reviews 5, no. 5 (2019): 20180114.
The paper discusses a technique called Metadynamics which can be used to estimate the binding free energy, it mentions the equations and procedure for this technique as well as a case study.
It also describes pharmacophores obtained from molecular dynamics simulations, otherwise known as dynophores. Finally, A procedure to find a representative pharmacophore model from a MD simulation is explained.