A Chemist’s Guide to Maestro

Tutorial Created with Software Release: 2026-2

Topics: Hit-to-Lead & Lead Optimization, Medicinal Chemistry Design, Small Molecule Drug Discovery

Products Used: Ligand Designer, Maestro

This tutorial is written for use with a 3-button mouse with a scroll wheel.

Tutorial Content

1. Creating Projects and Importing Structures
2. Visualizing a Protein-Ligand Complex
3. Drawing and Modifying Molecules
4. Generating and Visualizing Ligand Conformations
5. Aligning Structures
6. Ideating with the Ligand Designer
7. Sharing and exporting your work
8. Conclusion and references

1. Creating Projects and Importing Structures

1.1 Set up a project for this tutorial

1.2 Import structures from files

This tutorial uses three example systems to showcase a variety of workflows and targets. Sections 2–4 use a factor Xa structure which you will also see in some of our other tutorials. Section 5 uses structures and ligands for HIV 1 protease. Section 6 uses a ligand-receptor structure of CDK2.

You can download the files for this tutorial from the button at the top of this page or by going to https://www.schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/achemistsguidetomaestro.zip. Extract the zip archive to a convenient location, for example your project’s working directory.

Each section and sub-section will instruct you to import the appropriate files from the inputs subdirectory of the tutorial files into your Maestro project. You can either drag and drop them from the location you extracted the tutorial zip archive or use File > Import structures in Maestro’s menu bar. In addition to the required input files, the tutorial archive contains the outputs for all jobs you will run in this tutorial, as well as some optional data should you wish to explore a bit more.

2. Visualizing a Protein-Ligand Complex

The following interactive tutorials show step-by-step how to adjust the display of atoms in the Workspace and how to obtain different views of a binding pocket. For a more detailed walk through this process, see the Introduction to Structure Preparation and Visualization tutorial.

3. Drawing and Modifying Molecules

Maestro offers two complementary tools for building and editing molecules:

• 2D Sketcher — best for drawing molecules from scratch, making atom and bond substitutions, or pasting SMILES strings. It works like a chemical drawing program and automatically generates 3D coordinates when you save a sketch.
• 3D Builder — best for adding fragments to an existing 3D structure, deleting atoms, changing bond orders, or manipulating geometry directly in the Workspace.

The following two interactive tutorials show how to use each tool.

4. Generating and Visualizing Ligand Conformations

A single conformation (be it from a crystal structure or energy minimization) is only one snapshot of a molecule's conformational landscape. To understand what shapes a ligand can adopt in solution, during binding, or when comparing to analogs, you need a conformational ensemble. MacroModel's conformational search uses the Monte Carlo Multiple Minimum (MCMM) method to systematically sample torsional space and return low-energy conformers.

In this section, you will run a conformational search on the 1FJS ligand and then overlay the resulting conformers on a common rigid core to gain an understanding of its flexibility.

4.1 Generate conformers

Conformer generation methods in the Schrödinger suite

In addition to MacroModel, there are several other tools you could use for conformational sampling of ligand-sized molecules based on your goals and your system:

• ConfGen is a fast method for sampling bioactive-like conformations useful in screening contexts. See the Conformational Analysis for Small Molecules Using MacroModel and ConfGen tutorial for more details on how to use it.
• Molecular dynamics (MD): Both unbiased (‘free’) MD (tutorial) and metadynamics (tutorial) can be used to explore conformational space in solution at significantly higher computational cost but with higher fidelity.
• Prime: A protein-centric tool used for exploring conformations of protein loops or macrocycles. See the Prime Macrocycle Sampling panel documentation and the Drug Development with Macrocycles tutorial.

4.2 Compare the conformers by superimposing the structures

To now compare the conformers, you can align a part of the structure (the core) between all conformers and get an impression of the shapes accessible to the molecule.

Note that the alignment you will use here is rigid – each molecule is translated and rotated to best overlap the reference without changing its internal degrees of freedom so that we can compare the conformers. We will cover additional details and methods for ligand alignment in the next section.

Reproducibility of conformational search results

The conformational search we used uses stochastic (Monte Carlo) sampling, which means the exact set of conformers you obtain may differ between runs even with the same input and settings. The overall conformational profile should be similar, but individual conformer counts and geometries may vary. Pre-generated results from the tutorial files (csearch_1fjs_lig-out) are provided so that you can proceed with a consistent set of conformers if needed.

5. Aligning Structures

Maestro provides tools for aligning and comparing structures for both small molecules and proteins. For ligands, you can rigidly superimpose on a shared substructure or flexibly align to find the best shape overlap. For proteins, you can align by overall fold or by binding-site geometry. Note that alignment is a geometric comparison tool — it does not score steric fit, strain, or interactions. To evaluate how a modified ligand would actually sit in a binding pocket, use Ligand Designer (Section 6) or Glide docking (see the Glide Docking Tutorial).

Aligning peptides or macrocycles

Peptides or macrocycles (peptidic or otherwise) present a particular challenge for alignment algorithms due to their large number of rotatable bonds and/or restrained torsions. There are dedicated tools for aligning peptides and macrocycles, presented in the Preparing Cyclic Peptides and Aligning them to a Reference Structure tutorial.

5.1 Aligning Protein Structures

When aligning protein structures, different tools allow placing the focus on different areas of the protein. The most general and robust approach is using the secondary structure assignments to match structural elements implemented in the Protein Structure Alignment panel. As an alternative, you can use the Binding Site Alignment panel, which prioritizes matching residues that contact the ligand. This approach can be especially helpful when comparing the binding sites of only distantly related off-target proteins.

5.2 Aligning Ligand Structures

Aligning two or more ligands in 3D is useful in several contexts:

• During conformer analysis, you overlay different conformations of the same molecule on a rigid core to see which parts are flexible (as described in Section 4.2).
• With congeneric series (e.g in the context of preparing structures for FEP simulations), you superimpose two related molecules — typically sharing a common scaffold — to see exactly where their substituents diverge.
• And during scaffold hopping, you flexibly align structurally distinct molecules to assess whether they could present similar pharmacophoric features despite different chemistry.

Maestro provides two complementary tools for generic ligand alignment: Superposition (shown in section 4.2) performs a rigid overlay by matching a defined substructure (atoms are translated and rotated as a group, but conformations are preserved), while Ligand Alignment adjusts torsions during the fit to find the best achievable shape overlap. Choose Superposition when the input conformations are meaningful (e.g., extracted from crystal structures); choose Ligand Alignment when you want to ask "could these molecules look alike?".

6. Ideating with the Ligand Designer

Ligand Designer is the primary Maestro tool for interactive lead optimization. It works with a protein-ligand complex: you edit the ligand's structure in 2D or 3D, and Ligand Designer predicts where the modified ligand would bind by generating a new docked pose. This is far more rigorous than simply overlaying a modified ligand onto the original — the conformational search, scoring function, and post-docking minimization produce considerably more accurate predictions than a geometric superposition alone.

In addition to targeted, manual editing, Ligand Designer allows you to enumerate ligand ideas (e.g. by attaching R-groups) to satisfy specific receptor requirements, such as H-bond interactions with specific residues, efficiently filling the receptor cavity, or displacing unstable water molecules.This allows you to quickly explore the chemical space and get instant feedback on your ideas.

6.1 Generate new ligand ideas

In this section, you will analyze the binding site of CDK2 bound to a ligand which does not fill the pocket very efficiently, make a few modifications, and predict the resulting binding poses.

6.3 Triage ideas within the Ligand Designer or using the 2D viewer

You have now designed several ligand modifications with Ligand Designer. Before taking your ideas to the next stage (docking, FEP+), you want to choose the most promising ones to pursue. Here, we show two ways to achieve that: from within the Ligand Designer, or by comparing their structures and properties side by side in the 2D Viewer.

7. Sharing and exporting your work

This section will cover the most common ways to share your work with colleagues – as files or images.

8. Conclusion and references

In this tutorial, you learned the core Maestro workflows for small-molecule medicinal chemistry:

• Viewing protein-ligand interactions and the Ligand Interaction Diagram
• Drawing and modifying molecules with the 2D Sketcher and 3D Builder
• Exploring ligand conformations with MacroModel conformational search
• Comparing molecules by rigid superposition and flexible alignment
• Comparing protein structures by overall fold and binding-site geometry
• Evaluating chemical modifications with Ligand Designer's pose prediction
• Comparing and triaging ideas with the 2D Viewer
• Saving images and exporting structures for sharing and publication.