Search for tag: "autodock"

Viewing the Results of AutoDock Vina in Chimera - Part 3

How to save a PDB file of just the native ligand from the experimental structure, so you can overlay the native ligand structure with the docked ligand.

From  Keri Colabroy on May 28th, 2020 55 plays 0  

Viewing the Results of AutoDock Vina in Chimera - Part 2

Overlaying the docked poses with the native ligand

From  Keri Colabroy on May 28th, 2020 39 plays 0  

Viewing the Results of AutoDock Vina in Chimera - Part 1

Using ViewDock to look at the scores and poses of docked small molecule ligands in the target receptor

From  Keri Colabroy on May 28th, 2020 47 plays 0  

Preparing the Protein/Receptor in UCSF Chimera - Part 6 or 9 continued

Alternate way to select and delete a ligand from a protein structure - using the Cntrl + Left Click selection strategy

From  Keri Colabroy on May 27th, 2020 12 plays 0  

Preparing the Protein/Receptor in UCSF Chimera - Part 6 or 9

Deleting the existing/experimental ligand from the structure before docking

From  Keri Colabroy on May 27th, 2020 63 plays 0  

Preparing the Protein/Receptor in UCSF Chimera - Part 8

Draw the "box" in AutoDock Vina. Use a native or experimental ligand to help you locate and size the box.

From  Keri Colabroy on May 27th, 2020 85 plays 0  

Preparing the Protein/Receptor in UCSF Chimera - Part 7

Open AutoDock Vina, specify receptor, ligand and output location

From  Keri Colabroy on May 27th, 2020 93 plays 0  

Preparing the Protein/Receptor in UCSF Chimera - Part 5

Add a ligand to the Chimera session with the dock-prepped protein/receptor structure

From  Keri Colabroy on May 27th, 2020 9 plays 0  

Preparing the Protein/Receptor in UCSF Chimera - Part 4

Saving the Chimera session. Don't forget to type out a .py suffix for your file name.

From  Keri Colabroy on May 27th, 2020 58 plays 0  

Preparing the Protein/Receptor in UCSF Chimera - Part 3

Dock Prep of the Protein structure including charges

From  Keri Colabroy on May 27th, 2020 58 plays 0  

Preparing a ligand in Chem 3D - Part 5

Adding a heteroatom or other functional group, checking bond lengths and bond angles

From  Keri Colabroy on May 27th, 2020 7 plays 0  

Preparing a ligand in Chem3D - Part 4

Saving the structure as Chem3D and *.pdb files

From  Keri Colabroy on May 27th, 2020 9 plays 0  

Preparing a ligand in Chem3D - Part 3

Adding a formal charge

From  Keri Colabroy on May 27th, 2020 5 plays 0  

Preparing a ligand in Chem3D - Part 2

Checking bond lengths and angles, optional MM2 calculation

From  Keri Colabroy on May 27th, 2020 11 plays 0