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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 7 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 6 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 7 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 4 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 21 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 24 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 23 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 2 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 13 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 8 plays 0  

Preparing the Protein/Receptor in UCSF Chimera - Part 2

Selecting and hiding protein chains and small molecules

From  Keri Colabroy on May 27th, 2020 14 plays 0  

Preparing a ligand in Chem3D - Part 4

Saving the structure as Chem3D and *.pdb files

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

Preparing a ligand in Chem3D - Part 3

Adding a formal charge

From  Keri Colabroy on May 27th, 2020 3 plays 0  

Preparing a ligand in Chem3D - Part 2

Checking bond lengths and angles, optional MM2 calculation

From  Keri Colabroy on May 27th, 2020 4 plays 0  

Preparing a ligand in Chem 3D - Part 1

Drawing a structure in Chem3D

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

Tech Talks FA18: Digital Archives

From  Instructional Technology Media Services on November 29th, 2018 12 plays 0