2022 DOCK tutorial 1 with PDBID 6ME2

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UCSF Chimera is a software which aids the interactive 3D visualization, editing, and analysis of biological macromolecules.


(some info about DOCK)


(some info about the structure)

Required Software

(chimera, dock,...)

Seawulf: Getting Started

Basics of the Command Line/Terminal

Logging in and navigating Seawulf

File transfers to/from Seawulf

Chimera: Getting Started

Searching for/Downloading files from the PDB

The RCSB Protein Data Bank is a useful tool for searching for and downloading files containing the 3D structures of biological macromolecules. One can search for a molecule by using an exact 4 letter code (such as "6ME2") or by searching for a short description (such as "melatonin with ramelteon complex"). Note that there may be many molecules that fit a given description, so one may need to scroll through results shown after the search to find the one of interest.

(insert picture of PDB w/ search bar)

Opening and viewing PDB files

(show some screenshots and explain file types)

First-steps for visualizations in Chimera

(show how to change view settings (i.e., black vs. white background), how to select parts of the structure based on a number of criteria, color parts, delete parts, etc)

Saving sessions

(explain how to save all the configurations of a session)

Saving files: file formats

(explain mol2, pdb, etc, maybe some words about properly organizing folder structures and properly naming files in the process)

Dock Prep

Initial investigation/preparation

(put in here anything you notice when first opening up a sometimes messy structure--in 6ME2's case we had to remove detergents and water that were far from the of-interest binding site, handle non-standard amino acids, etc. Compare to the structure described in the literature to see if everything is accurate)

Isolating the ligand and receptor

(show how to create two separate files, one with just the ligand and one with just the receptor)

Adding Hydrogens

(show how to add hydrogens in the isolated structure files)

Adding Charges

(show how to add charges in the structures)