Answers.Body: <p>I don't think it is possible just from the docking scores. Docking scores are designed to give you an estimate of the binding affinity (entalphy), but they do not take entropic contributions into account very well. The best you can do are molecular dynamics simulations to calculate the free energy of binding. Which can be computationally quite costly e.g. with GROMACS or CHARMM.</p>
  <p>You can estimate the IC50 with molecular dynamics simulations as well, but that is not straightforward. E.g. with Umbrella simulations. An example for a potassium channel and a very simple ligand can be found <a href="https://www.mpibpc.mpg.de/278397/Wacker-Soeren_2008_diploma_thesis_Goe.pdf" rel="nofollow noreferrer">here</a>.</p>
  <p>Another approach would be to build a predictive model. If you have a library of compounds at hand you could use the chemical structures and e.g. the docking scores to estimate the IC50 based on statistics or machine learning. But biology is very messy in general, though if you get a representative dataset with very similar compounds to the one that you have in your dataset then you might be successful. You have to be sure that the binding site and pose are correct though.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-09-23T02:20:03.463Z
Answers.LastActivityDate: 2020-09-29T16:09:22.483Z
Answers.LastEditDate: 2020-09-29T16:09:22.483Z
Answers.UserDisplayName: Soerendip
Body: <p>How to predict the half-maximal inhibitory concentration (IC50) of my ligands.</p>
  <p>I'm currently using Schrodinger suite software and I don't know how to predict the IC50?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-23T17:45:59.323Z
Comments.Text: It is usually helpful to do a little research with a search engine or to give more information about what exactly you need. See e.g. https://www.schrodinger.com/kb/936
Comments.UserDisplayName: Maximilian Press
Tags: <docking>
Title: predict the IC50 after using Schrodinger suite Glide tool for docking
ThreadText: # predict the IC50 after using Schrodinger suite Glide tool for docking
  
  (Asked by: username_0 on 2020-09-18)
  
  How to predict the half-maximal inhibitory concentration (IC50) of my ligands.
  
  I'm currently using Schrodinger suite software and I don't know how to predict the IC50?
  
  **Tags:** docking
  
  > **Comments:**
  > **username_1**: It is usually helpful to do a little research with a search engine or to give more information about what exactly you need. See e.g. https://www.schrodinger.com/kb/936  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2020-09-23. Score: 2 | Accepted answer
  
  I don't think it is possible just from the docking scores. Docking scores are designed to give you an estimate of the binding affinity (entalphy), but they do not take entropic contributions into account very well. The best you can do are molecular dynamics simulations to calculate the free energy of binding. Which can be computationally quite costly e.g. with GROMACS or CHARMM.
  
  You can estimate the IC50 with molecular dynamics simulations as well, but that is not straightforward. E.g. with Umbrella simulations. An example for a potassium channel and a very simple ligand can be found [here](https://www.mpibpc.mpg.de/278397/Wacker-Soeren_2008_diploma_thesis_Goe.pdf).
  
  Another approach would be to build a predictive model. If you have a library of compounds at hand you could use the chemical structures and e.g. the docking scores to estimate the IC50 based on statistics or machine learning. But biology is very messy in general, though if you get a representative dataset with very similar compounds to the one that you have in your dataset then you might be successful. You have to be sure that the binding site and pose are correct though.
  
  
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