dockingvina
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dockingvina [2012/10/14 10:55] – rkiss | dockingvina [2014/03/29 20:58] (current) – [Limits] flack | ||
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====== Docking (Vina) ====== | ====== Docking (Vina) ====== | ||
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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, | 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, | ||
- | The Docking (Vina) workflow step utilizes the [[http:// | + | The Docking (Vina) workflow step utilizes the [[http:// |
===== When to use ===== | ===== When to use ===== | ||
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- | If you are new to docking, it is suggested to choose one of the ~10,000 prepared target structures. If you are more experienced, | + | If you are new to docking, it is suggested to choose one of the ~10,000 prepared target structures. If you are more experienced, |
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. [[propertyfilter|Property | + | 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 |
==== Options ==== | ==== Options ==== | ||
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== Selecting target == | == Selecting target == | ||
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When browsing the already available targets, you can search/ | When browsing the already available targets, you can search/ | ||
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== Target visualization == | == Target visualization == | ||
- | 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/ | + | {{: |
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+ | 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/ | ||
== Upload target == | == Upload target == | ||
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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:// | You can also run an automatic target preparation for docking by ticking the “Preparation” box, in which case, [[http:// | ||
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+ | 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/ | ||
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== Binding site center == | == Binding site center == | ||
- | X, Y and Z coordinates (from the coordinate system of the protein). These are automatically populated with values if they are present in the target database. Coordinates are available for all targets derived from the [[http:// | + | X, Y and Z coordinates (from the coordinate system of the protein). These are automatically populated with values if they are present in the target database. Coordinates are available for all targets derived from the [[http:// |
== Binding site area == | == Binding site area == | ||
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===== Results ===== | ===== Results ===== | ||
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* 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 Free 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.txt · Last modified: 2014/03/29 20:58 by flack