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dockingvina [2012/12/17 22:53] – [How to use] rkissdockingvina [2014/03/29 20:58] (current) – [Limits] flack
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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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 Docking results are ranked by docking scores (the more negative the better), which indicates how well the ligand is predicted to bind to the target. It is, however, also important to check the binding mode and analyze whether it is in agreement with a priori knowledge. Docking results are ranked by docking scores (the more negative the better), which indicates how well the ligand is predicted to bind to the target. It is, however, also important to check the binding mode and analyze whether it is in agreement with a priori knowledge.
  
-Since docking is one of the most computationally intensive drug discovery tools, it is highly recommended to apply it in the last steps in a screening workflow. [[mculepropertyfilter|mcule property filter]], [[reos|REOS filter]] and [[diversitysel|Diversity selection]] might be used to narrow down the search space to apply the Docking (Vina) step to the most interesting candidates only.+Since docking is one of the most computationally intensive drug discovery tools, it is highly recommended to apply it in the last steps in a screening workflow. [[basicpropertyfilter|basic property filter]], [[reos|REOS filter]] and [[diversitysel|Diversity selection]] might be used to narrow down the search space to apply the Docking (Vina) step to the most interesting candidates only.
  
 ==== Options ==== ==== Options ====
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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_vis.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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 You can also run an automatic target preparation for docking by ticking the “Preparation” box, in which case, [[http://autodock.scripps.edu/resources/adt|AutoDockTools]] will be utilized to add hydrogens on your target if none exists, add Gasteiger charges, merge charges and remove non-polar hydrogens, lone-pairs, water molecules and non-standard residues. If you opt out the automatic preparation, only a quick check for file validity will be performed. You can also run an automatic target preparation for docking by ticking the “Preparation” box, in which case, [[http://autodock.scripps.edu/resources/adt|AutoDockTools]] will be utilized to add hydrogens on your target if none exists, add Gasteiger charges, merge charges and remove non-polar hydrogens, lone-pairs, water molecules and non-standard residues. If you opt out the automatic preparation, only a quick check for file validity will be performed.
 +
 +Please note that the PDB upload file size limit is currently 2MB. If you have a larger PDB file, we suggest to extract and upload only the binding site or a single monomer/chain from the PDB file. You can extract monomers by any text editors. To reduce the file size, you can eliminate all lines and keep the ATOM records only. You can find the chain identifier after the three letter residue name (in the below example "PRO" is the residue and "A" is the chain identifier).
 +
 +{{:pdbextr.png?500|}}
 +
  
 == Binding site center == == Binding site center ==
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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
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 ===== Limits ===== ===== Limits =====
  
-The Docking (Vina) filter available in the [[freepackage|Free package]] is limited to 500 input molecules per month. If you need more, [[subscriptionpackages|subscribe]] to our Docking (Vina) package.+The Docking (Vina) filter available in the [[freepackage|Free package]] is limited to 10000 input molecules per month. If you need more, [[subscriptionpackages|subscribe]] to our Docking (Vina) package.
  
 ===== Docking protocol ===== ===== Docking protocol =====
  
 Docking (Vina) workflow step requires input ligands with a valid 3D structure, therefore the input ligand collection is prepared for docking as follows. Unknown or undefined tetrahedral stereocenters and cis-trans double bonds are converted into well-defined centers and double bonds by the stereoisomer generator of mcule. Molecules failed to dock are skipped. To ensure that molecule conversions did not affect the identity of the molecule, InChI strings of the docking input and output are compared and in case of InChI mismatch, the molecule is skipped. Docking (Vina) workflow step requires input ligands with a valid 3D structure, therefore the input ligand collection is prepared for docking as follows. Unknown or undefined tetrahedral stereocenters and cis-trans double bonds are converted into well-defined centers and double bonds by the stereoisomer generator of mcule. Molecules failed to dock are skipped. To ensure that molecule conversions did not affect the identity of the molecule, InChI strings of the docking input and output are compared and in case of InChI mismatch, the molecule is skipped.
dockingvina.1355784832.txt.gz · Last modified: 2012/12/17 22:53 by rkiss