2024 DOCK tutorial 2 with PDBID 1NDV

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Revision as of 15:38, 6 March 2024 by Stonybrook (talk | contribs) (Analyzing the Protein Structure:)
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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.

1ndv raw pdb.jpg

Coordination

1ndv coordination.jpg

Ligand

Surface Spheres

DMS file

sphgen

sphere selector

Gridbox

showbox

grid

Energy Minimization for Ligand

Footprint Generation

Rigid Docking

Fixed Anchor Docking

Flex Docking

Virtual Screening

Slurm

Cartesian Minimization

reScore