2024 DOCK tutorial 2 with PDBID 1NDV

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Revision as of 15:10, 6 March 2024 by Stonybrook (talk | contribs) (Protein)
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Introduction

Required Software

File Set-up

Preparing Structure Files

Protein

Open your protein pdb in Chimera. The pdb for 1ndv from rcsb.org is shown below:

Caption

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