As you will notice, the MDL graph is pretty similar to a standard graph, yet has some features & differences that makes it unique:

The nodes used in a MDL graph are specific.
a MDL graph can only have one single output called "root".
MDL graph introduces a new way to select & create nodes (see Contextual Node Creation below)
Exposing parameters differs from Standard Graph (See the Exposing a Parameter page)

MDL Graph Creation

In order to create an MDL Graph, follow these steps:

Create a new Substance package, or open an existing one.
In the explorer: right click on the package and click on new/

You can also click on the icon on the main toolbar:

You will then be prompted to choose a MDL preset:

Once you have chosen your template and named your graph, just click OK on the top right of the window: the MDL graph will be generated according to the selected template:

MDL Graph Parameters

Like a standard graph, there is 2 ways to access the graph parameters:

Click on the graph name in the Explorer view
Double-click on an empty space in the graph view

Parameters are subdivided in 3 sections:

Attributes
MDL Annotations
Graph Inputs

Attributes

Attributes are information used by Substance Designer itself

Identifier

Name displayed in the library

Show in Library

Defines if the MDL Graph should be seen in the Library or not

Icon

You can select a specific icon to display into the library.

MDL Annotations

Annotations provides extra meta information to the MDL:

Graph Inputs

This is the section where the parameters exposed by the user will appear:

In this page:

The MDL Graph