Answers.Body: <p>My answer is mainly based on molecular dynamics,but in this context it shouldn't make much of a difference.</p>
  
  <p>The main reason has to do with the <code>force-field</code>-<code>water</code> model used during the simulation. Examples of water models are <code>SPC</code>, <code>TIP3P</code> or <code>TIP4P</code>; same molecule (water) but different topology.</p>
  
  <p>A <code>pdb</code> usually comes from different sources and it can contain molecules that are not standard and therefore not recognised by the model of your simulation. Usually, once the structure is loaded, your system is <code>re-built</code> so that it conforms to the model topology. There are exception though, for example if your water is part of a functional active site. In that case you can keep it, but its structures (topology of the water molecule) has to be recognised by the model.</p>
  
  <p>Hydrogens are usually added to "saturate" and stabilise the bonds. </p>
  
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Answers.Text: Totally correct for MD. However, a wee note: most ligand docking program use implicit water (except special case such as WaterDock), which means that TIP3P waters or similar are not added, but a fudge factor is used to account for the dynamic but stabilising polar properties of water.
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Answers.Body: <h2>Hydrogens</h2>
  
  <p>Most crystallographic structures are X-ray and the hydrogens are absent. In the case of neutron diffraction models, there may be many missing high b-factor ones (<a href="https://michelanglo.sgc.ox.ac.uk/data/e5590567-3c91-4149-8ac1-275f64f1060c" rel="nofollow noreferrer">example in PDB:5MOP</a>). As a consequence models are reprotonated. Also missing carbons and missing loop residues are added for some in silico applications too (not docking).</p>
  
  <p>However, it is always good to manually tweak the protonation. In the case of enzymes with protanatable side chains in the active site, some reading is required to get the charges right: by default aspartates will be unprotonated, but they may be protonated (glutamic acid) in the active site and it is important to get it right (<em>cf.</em> <a href="https://blog.matteoferla.com/2018/09/everything-you-wanted-to-know-about.html" rel="nofollow noreferrer">this post about it</a>). Some times its the ligand parameterisation may give the physiologically incorrect protonation (<em>cf.</em> <a href="https://blog.matteoferla.com/2019/10/rdkit-for-rosetta-plp-ligand-space-as.html" rel="nofollow noreferrer">this post</a>).</p>
  
  <h2>Waters</h2>
  
  <p>Crystallographic waters can be important catalytically and structurally, but can be pushed out and actually it is a good thing: you have a hit that take its place. Polar bonds are stronger than hydrophobic ones and most types of &pi; bonding.</p>
  
  <p>Waters in most docking software is <code>implicit</code> and is modelled as a parameter in the force-fields —think of it as a ghostly watery haze. So a left behind water, not only will get in the way of the docked small molecule, it may for some programs cause issues as they will try to dock it. A notable exception is WaterDock mod for AutoDock, but the jury is out on whether it is better. Water is polarisable in reality in a very complex way (protonated (OH3+) or deprotonated (OH-) with very different charges) and most water models do not cut it and instead do not account for this.
  The way implicit waters are computed differs in some applications, which is also something to look into.</p>
  
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Answers.UserDisplayName: Matteo Ferla
Answers.Body: <p>The molecular docking programs usually tread the target structure as rigid. It does not know which atom belongs to the receptor and which is bulk water. So, if you keep the water in the structure the program cannot properly place the ligand there. </p>
  
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Body: <p>What is the reason for adding hydrogen and removing unnecessary water molecules from the protein structure before protein-ligand docking? FYI, the tools I used for docking is GOLD.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-27T08:18:40.423Z
Comments.Text: I think if you could add some more context it would be helpful to answer. Who said it is needed? Under which conditions are you looking for a docking? Sometimes  water is need in order to enable interaction or form stable bounds (AFAIK)
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-28T07:04:45.273Z
Comments.Text: No one say that but from the software, it say "delete water IF REQUIRED". I just don't understand what it meant by "IF REQUIRED" and when it is necessary to remove water or add hydrogen. Btw, from your reply, does it meant that sometime, water is required for an enzyme to function?
Comments.UserDisplayName: Zheng Keong Ng
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-28T08:12:18.473Z
Comments.Text: Yes, sometimes water is needed for an enzyme to function. When it is necessary to remove water is a hard question that depends on what environment are you simulating and the protein you are modelling
Comments.UserDisplayName: llrs
Tags: <protein-structure><docking><structural-biology>
Title: Why is it necessary to add hydrogen and delete water before protein-ligand docking?
ThreadText: # Why is it necessary to add hydrogen and delete water before protein-ligand docking?
  
  (Asked by: username_0 on 2019-03-27)
  
  What is the reason for adding hydrogen and removing unnecessary water molecules from the protein structure before protein-ligand docking? FYI, the tools I used for docking is GOLD.
  
  **Tags:** protein-structure, docking, structural-biology
  
  > **Comments:**
  > **username_1**: I think if you could add some more context it would be helpful to answer. Who said it is needed? Under which conditions are you looking for a docking? Sometimes  water is need in order to enable interaction or form stable bounds (AFAIK)  
  > **username_0**: No one say that but from the software, it say "delete water IF REQUIRED". I just don't understand what it meant by "IF REQUIRED" and when it is necessary to remove water or add hydrogen. Btw, from your reply, does it meant that sometime, water is required for an enzyme to function?  
  > **username_1**: Yes, sometimes water is needed for an enzyme to function. When it is necessary to remove water is a hard question that depends on what environment are you simulating and the protein you are modelling  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_2 on 2019-11-14. Score: 4
  
  My answer is mainly based on molecular dynamics,but in this context it shouldn't make much of a difference.
  
  The main reason has to do with the `force-field`-`water` model used during the simulation. Examples of water models are `SPC`, `TIP3P` or `TIP4P`; same molecule (water) but different topology.
  
  A `pdb` usually comes from different sources and it can contain molecules that are not standard and therefore not recognised by the model of your simulation. Usually, once the structure is loaded, your system is `re-built` so that it conforms to the model topology. There are exception though, for example if your water is part of a functional active site. In that case you can keep it, but its structures (topology of the water molecule) has to be recognised by the model.
  
  Hydrogens are usually added to "saturate" and stabilise the bonds.
  
  > **Comments:**
  > **username_3**: Totally correct for MD. However, a wee note: most ligand docking program use implicit water (except special case such as WaterDock), which means that TIP3P waters or similar are not added, but a fudge factor is used to account for the dynamic but stabilising polar properties of water.  
  
  ---
  
  ### Answer by username_3 on 2019-12-14. Score: 4
  
  ## Hydrogens
  
  Most crystallographic structures are X-ray and the hydrogens are absent. In the case of neutron diffraction models, there may be many missing high b-factor ones ([example in PDB:5MOP](https://michelanglo.sgc.ox.ac.uk/data/e5590567-3c91-4149-8ac1-275f64f1060c)). As a consequence models are reprotonated. Also missing carbons and missing loop residues are added for some in silico applications too (not docking).
  
  However, it is always good to manually tweak the protonation. In the case of enzymes with protanatable side chains in the active site, some reading is required to get the charges right: by default aspartates will be unprotonated, but they may be protonated (glutamic acid) in the active site and it is important to get it right (*cf.* [this post about it](https://blog.username_3.com/2018/09/everything-you-wanted-to-know-about.html)). Some times its the ligand parameterisation may give the physiologically incorrect protonation (*cf.* [this post](https://blog.username_3.com/2019/10/rdkit-for-rosetta-plp-ligand-space-as.html)).
  
  ## Waters
  
  Crystallographic waters can be important catalytically and structurally, but can be pushed out and actually it is a good thing: you have a hit that take its place. Polar bonds are stronger than hydrophobic ones and most types of π bonding.
  
  Waters in most docking software is `implicit` and is modelled as a parameter in the force-fields —think of it as a ghostly watery haze. So a left behind water, not only will get in the way of the docked small molecule, it may for some programs cause issues as they will try to dock it. A notable exception is WaterDock mod for AutoDock, but the jury is out on whether it is better. Water is polarisable in reality in a very complex way (protonated (OH3+) or deprotonated (OH-) with very different charges) and most water models do not cut it and instead do not account for this.
  The way implicit waters are computed differs in some applications, which is also something to look into.
  
  
  ---
  
  ### Answer by username_4 on 2019-11-10. Score: 0
  
  The molecular docking programs usually tread the target structure as rigid. It does not know which atom belongs to the receptor and which is bulk water. So, if you keep the water in the structure the program cannot properly place the ligand there.
  
  
  ---
  
  