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_posts/2023-11-8-Peptide-Docking-with-ADCP-2.md

@@ -15,5 +15,16 @@ The intent of the post is to introduce *to our lab members* the new features in
 
 # Overview
 
-This post includes our own examples of docking calculations for cyclic peptides and peptides with D-amino acids which have better support in ADCP v 1.1. The post-processing in AutoDock Vina, which we used for ADCP v1.0, is compared with the new post-processing protocol in this post using the OpenMM funtionalities that were embedded in ADCP v1.1. Lastly, because the minimization is performed in-vacuo, we want to recalculate the binding energy and free energy in Amber using an implicit solvation model. 
+This post includes our own examples of docking calculations for standard AA peptides, cyclic peptides and peptides with D-amino acids which have better support in ADCP v 1.1. The post-processing in AutoDock Vina, which we used for ADCP v1.0, is compared with the new post-processing protocol in this post using the OpenMM funtionalities that were embedded in ADCP v1.1. Lastly, because the minimization is performed in-vacuo, we want to recalculate the binding energy and free energy in Amber using an implicit solvation model. 
 
+# Table of Contents
+
+* [Example 1-1: Docking a Standard AA, 5-mer Peptide and Using OpenMM for Minimization]
+* [Example 1-2: Exporting Parameters and Coordinates from OpenMM into Amber for MM/GBSA Calculation]
+
+* [Example 2-1: Docking a Standard AA, 5-mer Peptide and Using Vina for Local Optimization]
+* [Example 2-2: Exporting Molecules from RDKit into Amber for MM/GBSA Calculation]
+
+* [Example 3: Docking a cyclice peptide containing a Disulfide Bond and Pose Selection]
+
+* [Example 4: Docking a peptide containing D-amino acids and Backbone Dihedral Validation]