How do I use Discovery Studio docking?

How do I use Discovery Studio docking?

Discovery Studio LibDock Tutorial

  1. Define the protein as the receptor molecule.
  2. Look for possible binding regions in the receptor.
  3. Modify the sphere radius of the active part.
  4. Open the process and modify the parameters.
  5. Run the molecular docking calculation and view the results.
  6. Browse docking poses.

What is Discovery Studio used for?

Discovery Studio is a suite of software for simulating small molecule and macromolecule systems. It is developed and distributed by Dassault Systemes BIOVIA (formerly Accelrys).

Is Discovery Studio Visualizer free?

The BIOVIA Discovery Studio Visualizer is a free, feature-rich molecular modeling application for viewing, sharing and analyzing protein and small molecule data.

How do you make a ligand in Discovery Studio?

All Answers (7)

  1. Ligand preparation. -Apply Force field from simulation tool. -Perform minimization from protocol. – save the molecule as .sd formate.
  2. Protein preparation. -Apply Force field from simulation tool. -Perform minimization from protocol.
  3. Perform the CDOCKER or other methods from ligand receptor interaction protocol.

How does Discovery Studio measure distance?

For measuring distance select two atoms at the same time by clicking once on both (remember that it is necessary to maintain pressed the Shift key while clicking if you want to add selection) then choose Structure | Monitor | Distance.

How do you superimpose proteins in Discovery Studio?

From the menu bar, choose Structure | Superimpose | By Sequence Alignment…. This opens the Sequence Alignment dialog. 1ppe is the reference molecule. On the dialog, select all of the poses in the Molecules to superimpose list.

How do I change the background color in Discovery Studio?

You can access this by clicking the bottom right + button and under the Workspace Layout section you can change the color.

How do you prepare protein for docking?

Prepare the ligand

  1. Like the protein, the ligand lacks hydrogen atoms.
  2. First, extract the ligand atoms from the PDB.
  3. Load the ligand structure into ADT using File > Read Molecule and select indinavir.pdb.
  4. Again, colour by atom type.
  5. Now we have to add polar hydrogen atoms.

Where is Rmsd value in Discovery Studio?

Load reference molecule >> structure>> RMSD>> set reference. Then drag docked molecule to the same window>> select it >> structure>> RMSD>> all atoms or heavy atoms. The RMSD will be shown to the Right side window. Hope this helps.

How does Discovery Studio calculate Rmsd?

All Answers (3) RMSD = root-mean-square-deviation. If one knows x, y, z coordinates of the corresponding atoms, one can calculate distances between them [distance = (dx**2 + dy**2 + dz**2)**0.5] . . . and having the distances, one can calculate RMSD . . .

How do I choose a ligand for docking?

In order to obtain accurate docking results you need to search for a protein structure with a chemically similar to your target compound, co-crystallized ligand. If this is not the case, the PDB structure with the highest enrichment value should be the most appropriate.

How do you superimpose two structures in PyMOL?

To align two 3D structures, first open them both in the same PyMOL session (and color them distinctly). Type in the command “align X, Y” and hit enter into the command bar. This will superimpose the structure of X onto Y.

How do I open Pdbqt in Discovery Studio?


  1. Open DS visualizer.
  2. Open “2bxa.
  3. In the “pdbqt” tab, you will see a dropdown in a new left panel showing different poses of the ligand named as model_0, model_1, and so on.
  4. Go to the receptor tab, here, “pdb” –> right-click on the blank space –> click “Paste” .

How do I delete water molecules in Discovery Studio?

Edit menu: delete selected molecule….

  1. Open any crystal structure in Chimera (for example PDB: 3U1I)
  2. Go to Select>>Residue>click on HOH (or any other nonstandard residues you want to delete)
  3. Go to Actions>>Atoms/Bonds>>delete (it will delete the selected HOH from the PDB)
  4. Then save it by clicking File>>Save PDB.

Why do we add hydrogen in docking?

The addition of hydrogen helps to find the hydrogen bond interactions and more favorable to us to find binding affinity of ligand against protein.

How do you choose ligands for docking?