Answers.Body: <p>You can visualize with Discovery Studio Visualizer and Schrodinger.
  Arpeggio and PLIP can generate output files of the different interactions.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-24T10:51:17.463Z
Answers.Text: Hey, thanks! already found that PLIP can do it and it works pretty well so I went for it.
Answers.UserDisplayName: djordje
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-24T08:25:23.957Z
Answers.LastActivityDate: 2020-04-24T08:25:23.957Z
Answers.UserDisplayName: BND
Body: <p>I have used DOCK software to dock 10 ligands into the protein structure.</p>
  
  <p>I want to generate a pdb file that contains all 10 binding modes of the ligands together with the protein. So all together in one pdb file.</p>
  
  <p>Now, what I want to know is when I give this file to LIGPLOT, is it possible to generate something like:</p>
  
  <p>%polar interactions XX
  %non-polar interactions XX
  %hydrogen interactions XX</p>
  
  <p>Is there a way to do it with LIGPLOT, if now is there some other software that can be recommended for this type of assessment?</p>
  
  <p>I have been having hard time, trying to find a way or software that can perform similar type of calculation and give me similar type of output that I want.</p>
  
  <p>Best</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-11T16:32:03.453Z
Comments.Text: "binding modes" --> "poses".
  
  You will need to do it programmatically. [This post for example use Python pymol](https://bioinformatics.stackexchange.com/questions/12862/extract-autodocked-protein-ligand-connections-programatically/12888#12888) for querying atoms. Can you use Python, Perl or Julia?
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-12T01:45:38.187Z
Comments.Text: Yeah, I assumed so, cus it tends to be a bit more complicated. Unfortunately, I cant say for my self that I know any of the three languages :(
Comments.UserDisplayName: djordje
Tags: <proteins><protein-structure><docking>
Title: Visualizing protein-ligand interactions with LIGPLOT or any other suitable software?
ThreadText: # Visualizing protein-ligand interactions with LIGPLOT or any other suitable software?
  
  (Asked by: username_0 on 2020-04-11)
  
  I have used DOCK software to dock 10 ligands into the protein structure.
  
  I want to generate a pdb file that contains all 10 binding modes of the ligands together with the protein. So all together in one pdb file.
  
  Now, what I want to know is when I give this file to LIGPLOT, is it possible to generate something like:
  
  %polar interactions XX
  %non-polar interactions XX
  %hydrogen interactions XX
  
  Is there a way to do it with LIGPLOT, if now is there some other software that can be recommended for this type of assessment?
  
  I have been having hard time, trying to find a way or software that can perform similar type of calculation and give me similar type of output that I want.
  
  Best
  
  **Tags:** proteins, protein-structure, docking
  
  > **Comments:**
  > **username_1**: "binding modes" --> "poses".  You will need to do it programmatically. [This post for example use Python pymol](https://bioinformatics.stackexchange.com/questions/12862/extract-autodocked-protein-ligand-connections-programatically/12888#12888) for querying atoms. Can you use Python, Perl or Julia?  
  > **username_0**: Yeah, I assumed so, cus it tends to be a bit more complicated. Unfortunately, I cant say for my self that I know any of the three languages :(  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-04-24. Score: 1 | Accepted answer
  
  You can visualize with Discovery Studio Visualizer and Schrodinger.
  Arpeggio and PLIP can generate output files of the different interactions.
  
  > **Comments:**
  > **username_0**: Hey, thanks! already found that PLIP can do it and it works pretty well so I went for it.  
  
  ---
  
  