Difference between revisions of "2025 Denovo tutorial 2 with PDBID 1XMU"
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=Input File= | =Input File= | ||
| − | ==Ligand with Dummy Atom== | + | ==Modify Ligand with Dummy Atom== |
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| + | Below shows the original ligand with hydrogen (mol2 file). Open chimera and select the atoms to delete. Save the mol2 file | ||
==DOCK6 input== | ==DOCK6 input== | ||
Revision as of 16:21, 24 February 2025
Contents
Introduction
This tutorial describes de novo method to refine ligand structure(s) using DOCK6. Rather than screening existing compounds, de novo refinement adds fragments based on known bioactive compounds, aiming to produce new ligands that bind more tightly to protein receptors than current options. This strategy is particularly valuable for:
- Improving suboptimal ligand binding profiles
- Overcoming resistance mechanisms
- Exploring novel scaffolds while maintaining critical pharmacophore features
In this tutorial, we will utilize PDB structure 1XMU - Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Roflumilast.
System Preparation
We first prepare a folder to contain all the input and output files for de novo refinement for 1XMU. This is the current directory structure under the upper directory dock6-1xmu.
Input File
Modify Ligand with Dummy Atom
Below shows the original ligand with hydrogen (mol2 file). Open chimera and select the atoms to delete. Save the mol2 file
DOCK6 input
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