Body: <p>I'm looking for some good molecular docking software (preferably, one that comes with a Python API). I obviously found Vina and that's been quite helpful but I was wondering if there's anything out there that's more accurate and reliable ? Since there's so much software and publications out there, I thought someone here might be aware of some things that may be overlooked.</p>
  <p>Thanks in advance !</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-16T12:36:15.653Z
Comments.Text: The Schrödinger suite has among the nice tools, Glide, a docking tool, which generally outperforms other docking tools in benchmarks, but it is expensive. Generally however there will be a couple of licences that could be borrowed floating around in a given department —always worth asking around. However, docking is inaccurate —full stop— thus is a numbers game, so if say one in ten is legit, then you buy 50 compounds for testing.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-16T13:57:48.420Z
Comments.Text: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-16T16:29:37.017Z
Comments.Text: The Bot has a good point: it's a topic of ample discussion heavily benchmarked (occasionally with biased benchmarks): nobody wants to write a review here. However, focusing on a particular task can help greatly get an answer on how to improve your docking task as good experimental setup can change things a lot and will beat Autodock Vina under a generic setup: Say you want to dock a library in the adenine site of a kinase vs. you want place a GTP instead of a non-hydrolysable analogue vs. you want to dock the native ligand in an enzyme.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-17T09:12:38.107Z
Comments.Text: Thanks very much for all the replies. I come from a wet-lab based background so I don't like docking myself but some reason it appears to be a requirement for workflow validation. So I thought if I'm going to add something I don't have confidence in, I might as well add the most accurate one I can. 
  
  The project is meant to be easily to modify to adapt to new scenarios so that's why the generic question.
Comments.UserDisplayName: apvn
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-19T15:40:36.060Z
Comments.Text: "Method A is better than B" is always tricky when they are utterly different and will always be rather biased (by both the experimenter and reviewer 2) and one could argue that if method B were done differently taking into account X it would win.
  The major improvement with docking one can get is feeding it more information, which if the method A uses already then that argument is rather strong.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-19T15:41:42.853Z
Comments.Text: Examples of improvements making the box restrictive to the active/binding/hinge site (there are too many question here on the lines of "Vina is telling me 30 Å width is too big but I am using the whole xstal cell").
  Constraining based on known binders.
  Dealing with isomers (stereo- and tauto-).
  Correcting the protonation of residues and of the ligand.
  Etc.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-19T15:46:34.697Z
Comments.Text: However, here it sounds like you want to do docking just because other have and it does not enrich your story —then don't muddle it: empirical results (xstal, assays etc.) trumps docking hands down. Those papers may just have the data handy as they did it in the planning step even if the docking is shown as a latter step in the final paper...
Comments.UserDisplayName: Matteo Ferla
Tags: <docking><cheminformatics>
Title: Good molecular docking software?
ThreadText: # Good molecular docking software?
  
  (Asked by: username_0 on 2022-07-16)
  
  I'm looking for some good molecular docking software (preferably, one that comes with a Python API). I obviously found Vina and that's been quite helpful but I was wondering if there's anything out there that's more accurate and reliable ? Since there's so much software and publications out there, I thought someone here might be aware of some things that may be overlooked.
  
  Thanks in advance !
  
  **Tags:** docking, cheminformatics
  
  > **Comments:**
  > **username_1**: The Schrödinger suite has among the nice tools, Glide, a docking tool, which generally outperforms other docking tools in benchmarks, but it is expensive. Generally however there will be a couple of licences that could be borrowed floating around in a given department —always worth asking around. However, docking is inaccurate —full stop— thus is a numbers game, so if say one in ten is legit, then you buy 50 compounds for testing.  
  > **username_2**: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.  
  > **username_1**: The Bot has a good point: it's a topic of ample discussion heavily benchmarked (occasionally with biased benchmarks): nobody wants to write a review here. However, focusing on a particular task can help greatly get an answer on how to improve your docking task as good experimental setup can change things a lot and will beat Autodock Vina under a generic setup: Say you want to dock a library in the adenine site of a kinase vs. you want place a GTP instead of a non-hydrolysable analogue vs. you want to dock the native ligand in an enzyme.  
  > **username_0**: Thanks very much for all the replies. I come from a wet-lab based background so I don't like docking myself but some reason it appears to be a requirement for workflow validation. So I thought if I'm going to add something I don't have confidence in, I might as well add the most accurate one I can.   The project is meant to be easily to modify to adapt to new scenarios so that's why the generic question.  
  > **username_1**: "Method A is better than B" is always tricky when they are utterly different and will always be rather biased (by both the experimenter and reviewer 2) and one could argue that if method B were done differently taking into account X it would win. The major improvement with docking one can get is feeding it more information, which if the method A uses already then that argument is rather strong.  
  > **username_1**: Examples of improvements making the box restrictive to the active/binding/hinge site (there are too many question here on the lines of "Vina is telling me 30 Å width is too big but I am using the whole xstal cell"). Constraining based on known binders. Dealing with isomers (stereo- and tauto-). Correcting the protonation of residues and of the ligand. Etc.  
  > **username_1**: However, here it sounds like you want to do docking just because other have and it does not enrich your story —then don't muddle it: empirical results (xstal, assays etc.) trumps docking hands down. Those papers may just have the data handy as they did it in the planning step even if the docking is shown as a latter step in the final paper...  
  
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  ## 0 answers
  
  