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dockingvina [2012/12/17 22:56] – rkissdockingvina [2013/01/14 08:53] – sanmark
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 ====== Docking (Vina) ====== ====== Docking (Vina) ======
  
-{{:docking4.png?800|}}+{{:docking4.png?700|}}
  
 Molecular docking is a method that predicts the binding orientation of one small molecule at the binding site of a target macromolecule (protein, DNA, carbohydrates, lipids, etc.) and estimates the binding affinity. Docking mainly consists of the following two steps: (i) pose generation, (ii) affinity prediction (scoring). During pose generation, the ligand is placed into the binding site by sampling its rotational and translational degrees of freedom. Subsequently, the affinity is estimated based on the generated pose. Molecular docking is a method that predicts the binding orientation of one small molecule at the binding site of a target macromolecule (protein, DNA, carbohydrates, lipids, etc.) and estimates the binding affinity. Docking mainly consists of the following two steps: (i) pose generation, (ii) affinity prediction (scoring). During pose generation, the ligand is placed into the binding site by sampling its rotational and translational degrees of freedom. Subsequently, the affinity is estimated based on the generated pose.
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 == Selecting target == == Selecting target ==
  
-{{:docking_select.png?800|}}+{{:docking_select.png?700|}}
  
 When browsing the already available targets, you can search/filter/rank the entries by PDB ID, Protein name, Organism name, UniProt Name/Accession ID/Taxonomic ID. Your previously uploaded targets will also appear here, but they can be deleted at any time (Click on “Delete” in the first column). Selection can be made by clicking on “Select” in the first column. To visualize the target, you can click on “View in 3D” under “Select”, which will open a new page with an interactive 3D visualization box containing the target. When browsing the already available targets, you can search/filter/rank the entries by PDB ID, Protein name, Organism name, UniProt Name/Accession ID/Taxonomic ID. Your previously uploaded targets will also appear here, but they can be deleted at any time (Click on “Delete” in the first column). Selection can be made by clicking on “Select” in the first column. To visualize the target, you can click on “View in 3D” under “Select”, which will open a new page with an interactive 3D visualization box containing the target.
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 == Target visualization == == Target visualization ==
  
-{{:target_vis2.png?800|}}+{{:target_vis2.png?700|}}
  
 By default, protein main chains are displayed as ribbons and sidechains as lines. Heteroatoms (if any) are displayed as sticks. You can use your mouse or touchpad buttons to rotate (Left button), zoom (Right button or Scroll or Shift+Left button), translate (Middle button or Ctrl+Left button) and slab (Ctrl+Right button). For 3D visualization we use the WebGL/Javascript based molecule viewer [[http://webglmol.sourceforge.jp/index-en.html|GLmol]]. If you experience any problems or your target is not displayed as it is shown on the Figure, you should [[webglhelp|verify that your browser supports WebGL]], or you need to enable it manually. We suggest to use the latest version of [[https://www.google.com/intl/en/chrome/browser|Chrome]] or [[http://www.mozilla.org/en-US/firefox/new|Firefox]] to get the highest level user experience. By default, protein main chains are displayed as ribbons and sidechains as lines. Heteroatoms (if any) are displayed as sticks. You can use your mouse or touchpad buttons to rotate (Left button), zoom (Right button or Scroll or Shift+Left button), translate (Middle button or Ctrl+Left button) and slab (Ctrl+Right button). For 3D visualization we use the WebGL/Javascript based molecule viewer [[http://webglmol.sourceforge.jp/index-en.html|GLmol]]. If you experience any problems or your target is not displayed as it is shown on the Figure, you should [[webglhelp|verify that your browser supports WebGL]], or you need to enable it manually. We suggest to use the latest version of [[https://www.google.com/intl/en/chrome/browser|Chrome]] or [[http://www.mozilla.org/en-US/firefox/new|Firefox]] to get the highest level user experience.
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 == Upload target == == Upload target ==
  
-{{:upload.jpg?500|}}+{{:upload.png?500|}}
  
 You can upload your own target by clicking on “Upload a file”. All uploaded files will remain private and won't be accessible by any other user. You can upload your own target by clicking on “Upload a file”. All uploaded files will remain private and won't be accessible by any other user.
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 ===== Results ===== ===== Results =====
  
-{{:docking_results.png?800|}}+{{:docking_results.png?700|}}
  
   * Conformers for the successfully docked molecules   * Conformers for the successfully docked molecules
dockingvina.txt · Last modified: 2014/03/29 20:58 by flack