Answers.Body: <p>One option I found was Frog2</p>
  
  <p><a href="https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Frog2" rel="nofollow noreferrer">https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Frog2</a></p>
  
  <p><a href="https://github.com/tuffery/Frog2" rel="nofollow noreferrer">https://github.com/tuffery/Frog2</a></p>
  
  <p>From an input of a <code>mol2</code> or <code>sdf</code> file it creates a plethora of conformers, which can be outputted as a <code>pdb</code> file</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-01T16:34:43.037Z
Answers.LastActivityDate: 2020-02-01T16:34:43.037Z
Answers.UserDisplayName: user2182857
Answers.Body: <h2>Open babel</h2>
  
  <p>The most commonly used tool is <code>open-babel</code> (obabel). It seems annoying that you have to specify the number of conformers, but this is because if you get something like retinol, the number of conformers is huge. The command from the <a href="https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html" rel="nofollow noreferrer">documentation</a> is:</p>
  
  <pre><code>obabel startingConformer.mol -O ga_conformers.sdf --conformer --nconf 30
     --score rmsd --writeconformers
  </code></pre>
  
  <p>An alternative argument is <code>--confab</code> which will pick each representative of a RMSD cutoff cluster.</p>
  
  <p>Do note that 2D representations and un-protonated molecules will need extra command line arguments.</p>
  
  <h2>RDKit</h2>
  
  <p>You can also generate conformers in RDkit, but I think this is beyond your requirements, but I thought it may be good to mention the essential compchem python library.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-03T09:40:40.880Z
Answers.LastActivityDate: 2020-02-03T09:40:40.880Z
Answers.UserDisplayName: Matteo Ferla
Body: <p>I have multiple ligands (in pdb format) which I want to try and dock to various proteins.</p>
  
  <p>But for each ligand I have only a single conformation (by which I meant the spatial relationship between it's atoms, not its position relative to the target protein).</p>
  
  <p>How do I generate other possible conformations?
  Is there a generally used tool for that? </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-01-31T20:59:35.450Z
Comments.Text: Still not clear what you mean by “pose”. You need to use standard scientific English on this site.  Do you mean structure? If not it shouldn’t be difficult to find a scientific paper that uses the correct term.
Comments.UserDisplayName: David
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-01-31T21:04:47.830Z
Comments.Text: Thanks.
  I see that these are properly referred to as conformations.
Comments.UserDisplayName: user2182857
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-01-31T21:14:58.053Z
Comments.Text: Ok. I assume that your ligands are peptides or proteins that can adopt different conformations. There may be software for doing this, but it will be quite sophisticated. Good luck.
Comments.UserDisplayName: David
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-01-31T21:27:20.913Z
Comments.Text: I'm going to migrate this because it's a better fit for Bioinformatics since it's about tools rather than the underlying biology, and I think you're more likely to get a good answer there. I'm only loosely aware of their policies there so you may need to make edits.
Comments.UserDisplayName: Bryan Krause
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-01-31T22:43:31.450Z
Comments.Text: @David ["Pose" is standard scientific English for macromolecular docking](https://en.wikipedia.org/wiki/Docking_(molecular)).
Comments.UserDisplayName: canadianer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-01-31T22:45:55.063Z
Comments.Text: @canadianer — I stand corrected, although wonder how many on this list are familiar with the term.
Comments.UserDisplayName: David
Tags: <pdb>
Title: How to generate conformations for a ligand for in silico screening?
ThreadText: # How to generate conformations for a ligand for in silico screening?
  
  (Asked by: username_0 on 2020-01-31)
  
  I have multiple ligands (in pdb format) which I want to try and dock to various proteins.
  
  But for each ligand I have only a single conformation (by which I meant the spatial relationship between it's atoms, not its position relative to the target protein).
  
  How do I generate other possible conformations?
  Is there a generally used tool for that?
  
  **Tags:** pdb
  
  > **Comments:**
  > **username_1**: Still not clear what you mean by “pose”. You need to use standard scientific English on this site.  Do you mean structure? If not it shouldn’t be difficult to find a scientific paper that uses the correct term.  
  > **username_0**: Thanks. I see that these are properly referred to as conformations.  
  > **username_1**: Ok. I assume that your ligands are peptides or proteins that can adopt different conformations. There may be software for doing this, but it will be quite sophisticated. Good luck.  
  > **username_2**: I'm going to migrate this because it's a better fit for Bioinformatics since it's about tools rather than the underlying biology, and I think you're more likely to get a good answer there. I'm only loosely aware of their policies there so you may need to make edits.  
  > **username_3**: @username_1 ["Pose" is standard scientific English for macromolecular docking](https://en.wikipedia.org/wiki/Docking_(molecular)).  
  > **username_1**: @username_3 — I stand corrected, although wonder how many on this list are familiar with the term.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2020-02-01. Score: 1
  
  One option I found was Frog2
  
  <https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Frog2>
  
  <https://github.com/tuffery/Frog2>
  
  From an input of a `mol2` or `sdf` file it creates a plethora of conformers, which can be outputted as a `pdb` file
  
  
  ---
  
  ### Answer by username_4 on 2020-02-03. Score: 1
  
  ## Open babel
  
  The most commonly used tool is `open-babel` (obabel). It seems annoying that you have to specify the number of conformers, but this is because if you get something like retinol, the number of conformers is huge. The command from the [documentation](https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html) is:
  
  ```
  obabel startingConformer.mol -O ga_conformers.sdf --conformer --nconf 30
     --score rmsd --writeconformers
  
  ```
  
  An alternative argument is `--confab` which will pick each representative of a RMSD cutoff cluster.
  
  Do note that 2D representations and un-protonated molecules will need extra command line arguments.
  
  ## RDKit
  
  You can also generate conformers in RDkit, but I think this is beyond your requirements, but I thought it may be good to mention the essential compchem python library.
  
  
  ---
  
  