Difference between revisions of "2024 DOCK tutorial 2 with PDBID 1NDV"
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== Preparing Structure Files == | == Preparing Structure Files == | ||
=== Protein === | === Protein === | ||
| − | Open your protein pdb in Chimera. | + | ====Analyzing the Protein Structure:==== |
| − | [[File:1ndv_raw_pdb.jpg|center|600px| | + | Open your protein.pdb in Chimera and assess the protein structure: |
| + | |||
| + | 1. Are there any missing loops? | ||
| + | |||
| + | 2. Are there any metal coordination atoms forming key interactions with the protein? | ||
| + | |||
| + | The .pdb for 1ndv from the RCSB Protein Data Bank is shown below. | ||
| + | |||
| + | [[File:1ndv_raw_pdb.jpg|center|600px]] | ||
| + | |||
| + | Coordination | ||
| + | |||
| + | [[File:1ndv_coordination.jpg|center|500px]] | ||
=== Ligand === | === Ligand === | ||
Revision as of 15:34, 6 March 2024
Contents
Introduction
Required Software
File Set-up
Preparing Structure Files
Protein
Analyzing the Protein Structure:
Open your protein.pdb in Chimera and assess the protein structure:
1. Are there any missing loops?
2. Are there any metal coordination atoms forming key interactions with the protein?
The .pdb for 1ndv from the RCSB Protein Data Bank is shown below.
Coordination
