Answers.Body: <p>The answer is &quot;Depends&quot;. But the best thing is always to look at what you ended up with and do some triaging before buying/synthesising anything. By triaging I mean filtering by its properties (<em>.e.g.</em> <a href="https://en.wikipedia.org/wiki/Lipinski%27s_rule_of_five" rel="nofollow noreferrer">Lipinski</a>, reactivity, synthetic feasibility <em>etc.</em> —discussed in <a href="https://bioinformatics.stackexchange.com/questions/12971/generate-ligands-candidates-based-on-protein-shape/12975">this Bioinfo SE question</a>).</p>
  <h2>Score</h2>
  <p>Regardless of docking software used, a forcefield free-energy score is a result of the scoring function used and of the properties of the molecule —including VENA which uses a hybrid score function.</p>
  <p>This score is <em>not</em>, but generally is set up to try to match, the actual phys-chem one.
  <a href="https://en.wikipedia.org/wiki/Gibbs_free_energy" rel="nofollow noreferrer">Gibbs free energy</a> is measured in kcal/mol (or less commonly in kJ/mol). A hydrogen bond is about 2 kcal/mol, a π-π bond 1 kcal/mol and a salt bridge 3. The average energy of a collision of RT water molecules is 0.6 kcal/mol.</p>
  <p>Therefore, if you dock multiple compounds (virtual library screen, VLS) you sort by free energy to see the strongest binders and consider the top ones.
  However, a catch is that this will be biased by MW.</p>
  <p>Also, it is useful to score the hits with a different program (say Gold or ICM-dock).</p>
  <h2>Ligand Efficiency</h2>
  <p>A variant metric that is employed when your hits vary in size and when they are over a given size (<em>e.g.</em> not fragments under 200 Da) is <a href="https://en.wikipedia.org/wiki/Ligand_efficiency" rel="nofollow noreferrer">Ligand Efficiency (LE</a>), which is the ratio of your score over the number of heavy atoms (<a href="https://www.nature.com/articles/nrd4163" rel="nofollow noreferrer">ref</a>).</p>
  <h2>Single compound</h2>
  <p>If you have a single compound and want to know if it binds acceptably, then this is a length-of-a-piece-of-string question as every compound has an affinity constant to a given protein, except most may be beyond their solubility. Initial hits will have µM affinity, while a lead will have nM affinity. However, a KD is not a ∆G and depends on your protein.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-12-17T14:32:50.577Z
Answers.LastActivityDate: 2020-06-30T15:49:58.143Z
Answers.LastEditDate: 2020-06-30T15:49:58.143Z
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Body: <p>What score value is considered acceptable when using Vina Autodock tool for molecular docking simulations?</p>
  
Tags: <docking>
Title: What score value is considered acceptable when using Vina Autodock tool for molecular docking simulations?
ThreadText: # What score value is considered acceptable when using Vina Autodock tool for molecular docking simulations?
  
  (Asked by: username_0 on 2019-12-17)
  
  What score value is considered acceptable when using Vina Autodock tool for molecular docking simulations?
  
  **Tags:** docking
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2019-12-17. Score: 1
  
  The answer is "Depends". But the best thing is always to look at what you ended up with and do some triaging before buying/synthesising anything. By triaging I mean filtering by its properties (*.e.g.* [Lipinski](https://en.wikipedia.org/wiki/Lipinski%27s_rule_of_five), reactivity, synthetic feasibility *etc.* —discussed in [this Bioinfo SE question](https://bioinformatics.stackexchange.com/questions/12971/generate-ligands-candidates-based-on-protein-shape/12975)).
  
  ## Score
  
  Regardless of docking software used, a forcefield free-energy score is a result of the scoring function used and of the properties of the molecule —including VENA which uses a hybrid score function.
  
  This score is *not*, but generally is set up to try to match, the actual phys-chem one.
  [Gibbs free energy](https://en.wikipedia.org/wiki/Gibbs_free_energy) is measured in kcal/mol (or less commonly in kJ/mol). A hydrogen bond is about 2 kcal/mol, a π-π bond 1 kcal/mol and a salt bridge 3. The average energy of a collision of RT water molecules is 0.6 kcal/mol.
  
  Therefore, if you dock multiple compounds (virtual library screen, VLS) you sort by free energy to see the strongest binders and consider the top ones.
  However, a catch is that this will be biased by MW.
  
  Also, it is useful to score the hits with a different program (say Gold or ICM-dock).
  
  ## Ligand Efficiency
  
  A variant metric that is employed when your hits vary in size and when they are over a given size (*e.g.* not fragments under 200 Da) is [Ligand Efficiency (LE](https://en.wikipedia.org/wiki/Ligand_efficiency)), which is the ratio of your score over the number of heavy atoms ([ref](https://www.nature.com/articles/nrd4163)).
  
  ## Single compound
  
  If you have a single compound and want to know if it binds acceptably, then this is a length-of-a-piece-of-string question as every compound has an affinity constant to a given protein, except most may be beyond their solubility. Initial hits will have µM affinity, while a lead will have nM affinity. However, a KD is not a ∆G and depends on your protein.
  
  
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