Teaching with Schrödinger

Updated: 1-23-22

Protein Ligand Docking
Created with: Release 2021-3
Prerequisites: working knowledge of Maestro
Files Supplied: Protein_ligand_docking_worksheet
Categories:
biochemistry, medicinal chemistry

About this Lesson
Determining the binding mode of an active molecule to a given protein target isimportant in the drug discovery pipeline. This lesson will focus on reproducing anexperimentally observed binding mode through docking.
Using Maestro, students will learn how to import a .pdb file of a crystal structure,
prepare a protein and ligand, as well as dock a ligand into a protein receptor using
Schrödinger’s Glide. They will also analyze protein-ligand interactions from a Ligand
Interaction Diagram.

Learning Objectives
Prepare ligand and protein structures in Maestro● Learn the steps of a molecular docking workflow using Schrödinger’s Glide● Analyze integral protein-ligand interactions within an active site using the Ligand
Interaction Diagram●

1
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Standards●

ACS Guidelines○●

ETS Chemistry GRE○●

Biological macromolecules (Section 5.1)
Organic Chemistry – Amino acids, Peptides (3F)

AAMC MCAT○

Structure, function, and reactivity of biologically-relevant molecules (5D)

Assessments
The following types of formative assessments are embedded in this lesson:●●

Assessment of student understanding through discussion of warm-up questions andfilling in any knowledge gaps about structure-based virtual screen steps
Visual assessment of student-generated docking scores from their own set of ligands

Warm-Up Questions: To be done on their own or at the beginning of class
Read the article “A systematic analysis of atomic protein-ligand interactions in the PDB” andanswer the following questions.
1) What are 7 of the most frequent protein-ligand interactions?

2) What is the most frequent protein family found in the protein data bank?

Lesson Outline
1. What you will need for this lesson - p. 3
2. Introduction to Protein Ligand Docking - p. 5
3. Preparing Protein Structures - p. 7
4. Preparing a Ligand Structure - p. 15
5. Generating a Receptor Grid - p. 19
6. Docking a Ligand - p. 23
7. Analyzing Docked Poses - p. 25
8. Visualizing Protein-Ligand Complexes - p. 27
9. Individual Exercise - p. 35
10. Summary, Additional Resources, and References - p. 36

2
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

1.

What you will need for this lesson
1. Go to the ‘Data’ folder and open yourClass Folder found on the virtual
cluster’s desktop.
2. Right-click on the folder called“Protein_Ligand_Docking” and copy
folder to Desktop● Here, you will find the lesson
plan, worksheet, and any
additional resources
3. Open Maestro
a. See Starting Maestro if you
need help

Figure 1-1. Open Maestro.
4. Go to File > Change Working
Directory
5. Find your “Protein_Ligand_Docking”
folder that you duplicated to yourDesktop, and click Choose

Figure 1-2. Change Working Directory option.

3
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

6. Next, go to File > Save Project As
7. Type “Docking_tutorial” and click
Savea. The project will be titled
Docking_tutorial.prj

Figure 1-3. Save Project panel.

Figure 1-4. Choose the best mouse option foryour set up.

8. Finally, check your Mouse Actions
a. PC : Edit > Customize Mouse
Actionsb. Mac : Workspace >Customize Mouse Actions
9. Make sure you have the best option
chosen for your set up. This lesson
was written with a three-button mousewith a scroll wheel, meaning the scroll
wheel is a button as well as a wheel. If
you do not have a mouse, choose
Trackpad.
10. Go to File > Get PDB
11. For PDB IDs, type 1fjs
12. Click Download○○

Figure 1-5. Get PDB File panel.

1FJS is loaded into theWorkspace
A banner appears

Note: Banners appear when files have been
imported, jobs incorporated into the Entry
List, or to prompt a common next step. Here,preparing the protein will be covered in thefollowing section.

4
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

2.

Introduction to Protein Ligand Docking

As more protein structures are determined experimentally using X-ray
crystallography or nuclear magnetic resonance (NMR) spectroscopy, molecular docking
is increasingly used as a tool in drug discovery. Molecular docking is often used to
predict the binding mode of a small molecule into a protein binding site. Understanding
the types of protein-ligand interactions gained from docking poses are fundamental in
drug design.

Figure 1. Workflow for Protein Ligand Docking
Figure 1 shows a schematic for how to prepare ligand and protein structures, anessential first step of modeling. Structure files obtained from the PDB, vendors, andother sources often lack necessary information for performing modeling-related tasks.
Unfortunately, even when working with a high-resolution x-ray crystallographic structure,researchers can spend considerable time and effort correcting common problems suchas missing hydrogen atoms, incomplete side chains and loops, ambiguous protonation
states, and flipped residues. Additionally, waters that are crucial for ligand binding may
also be missing from apo binding sites. Why would hydrogens, loops and side chains,
as well as waters be missing? Let’s break it down:
In crystallography, the X-ray beams are scattered off of electrons, and the only
electrons around a hydrogen atom are those participating in the covalent bond withanother atom. Additionally, the resolution of crystal structures tend to be greater than 1
angstrom. This is because of inherent dynamic fluctuations of a protein structure withina crystal and small variability between protein structures across different unit cells.
However, perhaps this issue will be a thing of the past with the advent of newtechniques and advancing of current methodologies.

5
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Loops and side chains of protein residues can often be missing as well from aprotein structure – especially crystal and CryoEM structures. There are two reasons forthis. The first is that these loops or side chains may access multiple different structuresin each of the molecules in the crystal structure. The average over all of thesemolecules results in no electron density. The second is that even within the crystal
structure, these residues or loops may be dynamic within each of the molecules thatmake up the crystals. For similar reasons, electron density cannot be observed throughscattering. To combat this, we will use Prime to construct and add back in missing loops
and residues in the lowest energy state. Finally, there may be high energy waters thatplay an important role in ligand binding that are not resolved in the PDB structure.
What is extra in protein structures? There are often molecules added in to help
aid in crystallography that are not biologically relevant. This list of molecules includes
small organic stabilizing agents like glycerol and metals like Copper and Zinc.
Additionally, sometimes to help with X-ray diffraction, methionines are replaced withselenomethionines since selenomethionines are able to diffract X-rays better with theirelectron rich outer shells of selenium. Finally, if there are any chains in the structures(other proteins that were added to stabilize the protein of interest), it might be useful toremove these chains before performing docking or structure-based drug discovery.
In order to make these structures suitable for modeling tasks, we use the Protein
Preparation Workflow to resolve issues. Similarly, ligand files can be sourced fromnumerous places, such as vendors or databases, often in the form of 1D or 2D
structures with unstandardized chemistry. LigPrep can convert ligand files to 3D
structures, with the chemistry properly standardized and extrapolated, ready for use fordocking. We will go into more detail on these Maestro panels and workflows throughout
the lesson.
Here, we will reproduce an experimentally observed binding mode of 1FJS,
which is a serine protease that catalyzes the conversion of prothrombin to thrombin, thefirst joint step that links the intrinsic and extrinsic coagulation pathways. In this example,
the binding pocket has an ideal protein conformation to dock the ligand. Docking otherscreening ligands may present itself with more complications since they may preferbinding to a different protein conformation. See the lesson on Structure-Based Virtual
Screening to learn more.

6
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

3. Preparing Protein Structures for Glide Docking
Model
The Protein Preparation Workflow is run within the Preparation Workflow tab. The
workflow has processing, modification, and refinement tools that we will use on the
1FJS.pdb structure. This tool is intended to support two main workflows - interactive,
single protein preparations and highly-automated bulk protein preparations. Interactive
preparations are manually performed in a step-by-step manner, with the opportunity toreview the results of each step and easily control the order of modifications. Automatic
preparation is pre-set by the user by the use of toggles that control which stages of theworkflow are run in a single job. The Automatic workflow allows processing of multiple
protein structures in a single job, permitting they maintain the same settings. The
recommended minimal processing tasks are checked by default in both workflows but
may be modified using the dropdown options. There are also options for filling in
missing side chains and/or loops, depending on the needs of your structure. For more
information see Protein Preparation Workflow Panel Help.
The Protein Preparation Workflow toggles include Preprocess, Optimize H-Bond
Assignments, and Clean up. The Preprocess step fixes structural defects and adds
missing information. The Optimize H-bond Assignment section is used for optimizing
the hydrogen bonding network – a process that samples water orientations and flips
Asn, Gln, and/or His side chains at a specified pH value. Adjusting the pH will change
the protonation states of residues and ligands accordingly and is useful if you want toaccurately reflect the experimental conditions. The Clean Up section fixes clashes thatcan occur with adding hydrogens or filling missing sidechains. By default, an RMSD of
0.3 Å is used, minimizing both the hydrogens and heavy atoms via harmonic penalty
constraints. Optionally, hydrogen-only minimization can be chosen.
The Preparation Workflow tab may be used in conjunction with the Diagnostics tab andSubstructures tab. These tabs are intended for diagnosis and analysis of the protein
after preparation steps because automatic procedures cannot cover all possible cases.

7
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

3.1

Prepare the Protein using the Protein Preparation Workflow
1. In the Favorites toolbar, click
Protein Preparation○ The Protein Preparation
Workflow opens

Figure 3-1. The Protein Preparation
Workflow in the Favorites toolbar.

Figure 3-2. The Protein Preparation
Workflow in Automatic mode.

Note: You can also click Prepare in thebanner or find the Protein Preparation
Workflow in the Task Tool
2. In the Preparation Workflow tab,confirm the INTERACTIVE button
is off○ When on, the pane will readProtein Preparation
Workflow (interactive)
Note: INTERACTIVE mode can be used
for exploring manual options, or to run asingle protein in a step-by-step manner.
This tutorial will be running an automatic
protein preparation.

8
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

3. In the Specify Protein section,choose use structures from:Workspace
4. Select Global Settings○ A dropdown opens showing
the simulation pH and the
PDB pH as well as small
molecule options

Figure 3-3. Specify the protein from theWorkspace.

○ The Non-water solvents
option is left unchecked.
This saves computational
resources because theglycerols in our Workspace
will not be prepared
Note: The Specify Protein tool provides
you with the option to prepare a proteinfrom the Workspace, Project Table, File,or directly from the PDB.
5. Select Review Structure○ The substructures tab
opens to show Ligands,
Metals, Other, Waters, andChains9
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

6. Under Chains, click Chain L○ The Workspace zooms to
the chain
7. Click Delete from Entry○ The smaller of the two
chains is removed, and a
new entry appears in the
Entry List.
Note: Unless specified, waters andglycerols (GOL) belonging to chain L will
not be removed. Glycerols are a
crystallographic artifact with no biologicalrelevance. The Select dropdown provides
shortcuts for selecting these species
based on their proximity to specified
chains. Removing waters and glycerols
will be available again in the Clean Up
and Analysis steps
Figure 3-4. Review the structure forpreparation in the Substructures tab.

10
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

8. Select the Diagnostics tab○ Valence errors were found,but these bond order issues
will be resolved in theprotein preparation○ The Missing tab is empty,
indicating there are no
missing side chains in theprotein structure
9. Select Reports to view otherissues with the protein that must
resolved prior to modeling

Figure 3-5. View protein issues in the
Diagnostics tab
10. Return to the Preparation
Workflow tab
11. Confirm Preprocess is toggled on○ Notice Fill in missing side
chains is checked bydefault. If these were
missing in our structure
they would become
populated during this step
12. Under Preprocess, select More
Options○ Among the options
provided, notice that11
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Figure 3-6. Preprocess default settings

missing loops may be filled
in using Prime
13. Check the pH range for generating
het states with Epik
○ This should align with thephysiological or assay pH.
Note: Depending on your system andresearch question, you may want to keep
certain waters. See Protein Preparation
Workflow Panel Help for more details.

Figure 3-7. Optimize H-Bond Assignment
default settings

14. Confirm Optimize H-bondAssignment is toggled on
15. Click Settings○ Overlapping atoms causedby the addition ofhydrogens during thePreprocess step will becorrected, and side chains
may be flipped when thisjob is run
16. Check the pH for Optimization○ This value should be
captured in the pH range
chosen during thePreprocess step

12
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Figure 3-8. Clean Up default Settings

17. Confirm Clean Up is toggled on
18. Click Settings○ Notice that by default
distant waters will be
removed. The specified
distance to ligands can be
modified
19. Change the job name to
1FJS_Prepared
20. Click Run○ This job will take a few
minutes as all toggled jobs
are running consecutively○ A new group will be added
to the Entry List
21. In the Entry List, click 1FJS –prepared

Figure 3-9. Select the protein preparation
outputNote: In Interactive mode, multiple entries
will be added to the Entry List as eachindividual preparation task will be run as
an independent job

13
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

22. Return to the Protein Preparation
tool
23. Click the Substructures tab
24. Choose Reload from Workspace
25. In the Hets table, shift-click to
select all GOL rows
26. Click Delete from Entry
27. In the Waters table, shift-click to
select all waters
28. Click Delete from Entry

Figure 3-10. Perform Substructure
Review

Figure 3-11. Confirm issues have been
resolved during preparation

Note: These waters could have been
removed during the Clean Up processing
step. Depending on your system andresearch question, you may want to keep
certain waters. See Protein Structure
Preparation using the Protein Preparation
Workflow or Protein Preparation
Workflow Panel Help for more details.
1. In the 1FJS_Prepared-out1 group,
select 1FJS – with-deletions
2. Return to the Protein Preparation
Workflow and click the
Diagnostics tab to make surethere are no issues missed during
the preparation. You may need toclick Check Workspace Entry
3. Exit the Protein Preparation
Workflow14
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Note: If issues persist after preparation,
perform specific interactive protein
preparations on the modified protein withadjusted settings. The job type will
depend on which problems were found.
Question #1:
List one error that you identified to be a problem prior to running the Protein
Preparation Workflow.

4.

Preparing a Ligand Structure

In this section, we will prepare the co-crystallized ligand from the 1FJS structure for use
in virtual screening. This is a typical step for cognate ligand docking, as it provides
important validation prior to screening a larger ligand data set.
The following steps provide an example of how you would prepare a ligand data set
using LigPrep. Ligand files can be sourced from numerous places, such as vendors or
databases, often in the form of 1D or 2D structures with unstandardized chemistry.
Before being used in a virtual screen, ligands must be converted to 3D structures, with
their chemistry properly standardized and extrapolated.

4.1

Split the prepared structure
1. In the Entry List, double click 1FJS
- with-deletions in the
1FJS_Prepared-out1 group andrename the entry to
1FJS_prepared_dry
2. right-click on 1FJS_prepared _dry
3. Choose Split > Into Ligands,
Water, Other○ Two new entries appear in
the Entry List

15
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Figure 4-1. Right-click to split an entry
into different components.

4.2

4. Include 1FJS –prepared_dry_ligand○ Only the ligand is displayedin the Workspace

Run LigPrep
1. Go to Tasks > Browse > LigPrep○ The LigPrep panel opens

Figure 4-2. LigPrep application in the
Task toolbar.

16
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

2. For Use structures from, choose
Workspace (1 included entry)
3. Under Stereoisomers, choose
Determine chiralities from 3D
structure
4. Change Job name to ligprep_1fjs
5. Click Run○ A banner appears when thejob has been incorporated○ A new group is added to
the Entry List
○ The number of ligands inthis group is shown inparentheses
Note: The Tile functionality is very usefulfor seeing the slight variations inchemistry for the generated structures.
The Tile View can be turned on byclicking thein the Workspace
Configuration Toolbar in the bottom rightcorner and then clicking the Tile button.

➕

Figure 4-3. The LigPrep panel.

17
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

6. Type Ctrl+T (Cmd+T) to open the
Project Table
7. Click Tree to open the Property
Tree○ Different calculated
properties can be toggled
on and off○ Click the arrow next toeach application to view
more properties
Figure 4-4. The Project Table with theProperty Tree open.
Question #2:
Preparing a ligand using LigPrep may produce multiple output structures for each input
structure by generating different protonation states, stereochemical outcomes,
tautomers, and ring conformations. Why is it important to prepare a ligand before
proceeding with docking?

18
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

5.

Generating a Receptor Grid

Grid generation must be performed prior to docking with Glide. The shape andproperties of the receptor are represented in a grid by fields that become progressively
more discriminating during the docking process. To add more information to a receptor
grid, different kinds of constraints can be applied during the grid generation stage. For
a comprehensive overview of constraint options, see the grid generation videos on our
website or the Glide User Manual (Help > Help > User Manuals > Glide User
Manual). In this tutorial, we will set a hydrogen bond constraint in our receptor grid.

5.1

Identify the binding site

Figure 5-1. Receptor Grid Generation
option in Receptor-Based Virtual
Screening.

Figure 5-2. The Receptor tab of Receptor
Grid Generation.

1. Click the In circle next to
1fjs_prep_complex to include it in
the Workspace
2. Double-click Presets○ 1fjs_prep_complex isrendered using the Custom
Preset
3. Go to Tasks > Browse >Receptor-Based Virtual
Screening > Receptor Grid
Generation○ The Receptor Grid
Generation panel opens
4. Under Define Receptor, check theboxes for Pick to Identify theligand (Molecule) and Show
Markers○ A banner in the Workspace
will prompt you to click on
an atom in the ligand

19
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

5. Click on the ligand○ The ligand is now
highlighted with a purple
box around it○ The ligand will be excluded
from the grid generation
Note: The purple bounding box defines
the region that the docked molecule(s)can occupy to satisfy the initial stages of
docking

Figure 5-3. The ligand is defined to be
excluded from grid generation.

5.2

Define the bounding box dimensions
1. Click the Site tab
2. Select Centroid of Workspace
ligand (selected in the Receptortab)
3. Click Advanced Settings○ A green inner bounding box
appears

Figure 5-4. The Site tab of Receptor Grid
Generation.

Note: The green bounding box defines
the region in which the centroid of thedocked molecule(s) must occupy to pass
the initial stages docking

20
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

4. Adjust the settings for X, Y, and Z
sizes to 10, 8, and 6 Å ,respectively.
○ The shape of the green box
is changed
5. Click OK

Figure 5-5. Ligand diameter midpoint box
panel.

5.3

Set a hydrogen bonding constraint
1. Type L to zoom to the ligand
2. In the Structure Hierarchy, click
the magnifying glass
3. In the search field, type ASP 189
4. Select ASP 189

Figure 5-6. Search in the Structure
Hierarchy.

Note: Please see the Introduction to
Structure Preparation and Visualization
tutorial for instructions on how to add
residue labels and show H-bonds
5. Under Fit, click Fit view toselected atoms

Figure 5-7. Zoom to selected atoms.

21
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

6. In the Receptor Grid Generation
panel, click the Constraints tab
7. Click the H-bond/Metal (0) tab○ A banner appears
prompting selection of thereceptor atom to be theconstraint

Figure 5-8. The Constraints tab of
Receptor Grid Generation.
8. Click an oxygen atom of the ASP
189 sidechain○ Both oxygens arehighlighted○ An H-bond constraint isdefined in the Receptor
atoms table

Figure 5-9. Constraint defined on ASP
189.

22
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

9. Change Job name toglide-grid_1fjs
10. Click Run○ This job will take about aminute○ A folder named
glide-grid_1fjs is written to
your Working Directory

Figure 5-10. Run receptor grid generation
job.
Question #3:
Why is it necessary to generate a receptor grid? What would happen if you proceededwith docking a ligand without a receptor grid?

6.

Docking a Ligand

The minimum requirements for running a Glide virtual screen are a grid file and a ligand
file. It is strongly recommended that the grid file be generated from a protein preparedusing the Protein Preparation Workflow and the ligand file be prepared using LigPrep.
Additionally, you can choose the scoring function, set ligand- and receptor-based
constraints, and define the output. Please see the Glide User Manual for more detail. In
this section, we will include the hydrogen bonding constraint that was created in theprevious step.

23
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

In this section, we will dock the cognate ligand. The information gained from this step
can help with evaluating poses and beneficial interactions, which is useful for future hit
finding. This job will use the receptor grid file that was generated in the previous step.
1. Go to Tasks > Browse >Receptor-Based Virtual
Screening > Ligand Docking○ The Ligand Docking panel
opens
2. Next to Receptor grid, click
Browse and choose
glide-grid_1fjs.zip

Figure 6-3. The Ligands tab of the Ligand
Docking panel.

3. In the Ligands tab, for Use ligands
from, choose Files
4. Next to File name, click Browse
and choose
ligprep_1FJS-out.maegz

5. Click the Constraints tab
6. Click on the Grid-based tab
7. Under Use, check the H-bondconstraint for ASP 189
8. Change Job name toglide_1FJS_cognate
9. Click Run○ This job takes about aminute○ A banner appears to showthat files have been
incorporated○ A new group is added to
the Entry List
Figure 6-4. The Constraints tab of the24
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Ligand Docking panel.
Note: The 1fjs_prep_complex entry isfixed in the Workspace, the top
1fjs_prep_lig entry is included, and thePose Viewer panel appears
10. Include other ligand results○ H-bonds to ASP 189 areconserved
11. Double-click Presets
12. Double-click the In circle next to
1fjs_prep_complex○ The entry is no longer fixedin the Workspace

Figure 6-5. Binding pose of the top
docked cognate ligand (pink) comparedto the crystal structure (gray).

7.

Note: Though only the top ranked result
is in strong agreement with the
crystallographic pose, all three results
accurately capture the pose of the ligand
in the binding site (with varying degrees
of success in capturing the solvent
exposed region)

Analyzing Docked Poses

Multiple Glide docking results can be viewed in the Entry List and be identified by the
job name. Docked results will show the receptor in the first row and the docked
ligand(s) in the subsequent row(s), where they are ordered by best to worst docking
score, or Glide Gscore if Epik state penalties were not applied in LigPrep. The Glide
Gscore is broken down by van der Waals electrostatic components and can be seen in
the Project Table, using the Property Tree. You can read more about how docking
scores/poses are generated here and here and what dependencies they have here andhere.
25
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

7.1

Visualize the results using Pose Viewer

Figure 7-1. Pose Viewer panel.

7.2

1. Step through the results using theright and left arrow keys
○ Ligand poses are displayedin the Workspace○ Residues are coloredaccording to theirinteraction energies, ranging
from green (favorable) to red(unfavorable)
2. Close the Pose Viewer panel

Analyze the results

Figure 7-2. Glide Primary properties
shown in the Project Table.

1. In the Project Table, click theProperty Tree icon
○ The Property Tree appearson the right of the ProjectTable
2. Click the All box twice○ All boxes are deselected
3. Click the Glide box
4. Click Primary○ Only the Glide Primary
properties are shown
Note: Please see Knowledge Base Article
1027 for more information on the
difference between docking score, Glide
gscore, and glide emodel score.

26
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

8.

Visualizing Protein-Ligand Complexes

In this section, we will explore ways to visualize structures in the Workspace. Object
representation can be changed in a number of ways using the Style toolbox. Presets
offer the ability to quickly render a structure in a number of styles, similar to PyMOL, tofacilitate easy visualization. Presets can be used in a variety of ways, from de-cluttering
your structure to creating publication-quality images. We will analyze the protein-ligand
complex by looking at the interactions, and generate a custom set for some binding
residues of interest. Finally, we will visualize the surface of the binding pocket and lsave an image of the complex.

8.1

Use the Style toolbox

Figure 8-1. The Style toolbox with CPK
representation highlighted.

1. Include entry 1FJS – prepared
2. Type L○ The Workspace zooms to
the ligand
3. Under Quick Select, click L○ The ligand is selected
4. Click Style
5. Choose CPK representation○ The ligand is rendered inspace-filling (CPK)
representation○ This is only applied to theligand, since nothing else is
selected in the Workspace27
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

6. Click the Color Atoms arrow
7. Choose Element (Custom
Ligand), and pick orange from thesecondary menu
○ Ligand carbon atoms areorange8. Under Quick Select, click P○ The protein is selected
9. Type Z○ The Workspace is zoomed
to view the selectedstructure
10. In the Style toolbox, click Ribbons○ Ribbons are added to theproteinFigure 8-2. The Color Atoms menu.

28
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

11. Right-click on the ribbon○ The Edit Ribbon panel
opens
Note: Use the predictive highlighting toknow when you will click on the ribbon.
12. Click Residue position in thecolor scheme
13. Choose Single Color
Note: Click the box to the right of thecolor scheme to choose different colors

Figure 8-3. The Edit Ribbon panel.

29
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

8.2

Apply a Preset style
1. Click Presets
2. Choose Pretty○ The Workspace is renderedwith ribbons, a green
thick-tube ligand, and side
chains are hidden
3. Double-click Presets○ The Workspace is redrawn
with the Custom Preset○ The Workspace zooms to
the ligand

Figure 8-4. The Presets menu.

8.3

Visualize Interactions
1. In the Workspace Configuration
Toolbar, right-click Interactions○ The Interactions panel
opens
2. Turn on Non-covalent bonds
3. Turn off Pi-cation interactions
Note: Clicking the color to the right ofeach interaction opens the Preferences
panel, where the interaction visualization
can be customized
Note: The threshold for Contacts/Clashes
is set to 0.89 for bad and 0.75 for ugly.

30
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Figure 8-5. The Interactions panel in theWorkspace Configuration Toolbar.

8.4

These values correspond to the ratio ofthe distance between the two atoms andthe sum of their Van der Waals radii.

Generate and manipulate a surface
1. Under Quick Select, click … andchoose Binding Sites
2. Click Style and choose Surface○ A solid gray surface isapplied○ An S is next to the title in
the Entry List, click to see
surface options

Figure 8-6. More options in Quick Select.

Note: Click Surface (Binding Site) in theFavorites toolbar to perform the sametask

31
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

3. Right-click the surface
4. Choose Display Options○ The Surface Display
Options panel opens
5. For Color Scheme, choose
Electrostatic Potential
6. Change the Min and Max values to-0.1 and 0.1, respectively
7. Click OK○ The intensity of the surface
colors is increased

Figure 8-7. The Surface Display Options
panel.

8.5

Generate a 2D interaction diagram
1. In the Favorites toolbar, click
Ligand Interaction○ The 2D Workspace - Ligand
Interaction Diagram opens

Figure 8-8. Ligand Interaction Diagram in
the Favorites toolbar.

32
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

2. Check Sync with 3D and rotate
the ligand in the Workspace○ Ligand orientation ischanged in the 2D
representation
3. Choose View > LID Legend
Note: Images can be saved via File >Save Screenshot

Figure 8-9. The Ligand Interaction
Diagram with Sync with 3D turned on and
LID legend open.

8.6

Note: The residue icon point indicates the
direction of the sidechain

Save an image of the Workspace
1. Go to Workspace > Save ImageAs○ The Save Image panel
opens
2. Click Options >>3. Check Transparent backgroundand select 300 DPI
4. Change File name to
1FJS_binding_site
5. Click Save
○ A .png image of theWorkspace is saved to yourWorking Directory

Figure 8-10. Save Image panel withexpanded Options shown.

Note: If an item is highlighted in theWorkspace, the image is saved with theselection highlights

33
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Note: Go to Tasks > Browse >Workspace and Project Table
Operations for more image options,
including Ray Trace
Question #4:
What important protein-ligand interactions do you see when the cognate ligand isdocked? Take a screenshot of the Ligand Interaction Diagram below. List specificresidues and define specific interactions that may play an important role in binding.

34
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

9.

Individual Exercise

Part A:
Perform the same preparation steps on the 2XIR crystal structure. What were some of
the issues with this PDB structure from the first step of protein preparation?

Part B:
Search the Protein Data Bank for another protein-ligand complex and do the following:a) Import the .pdb file into Maestrob) Split the structure into Ligands, Waters, and Receptorc) Prepare the protein using the Protein Preparation Workflowd) Prepare the ligand using LigPrepe) Detect the binding site using Receptor Grid Generation

Dock all the conformations and tautomers generated from LigPrep back into the
prepared protein using Schrödinger’s Glideg) Take a screenshot of your docking results including the docking score and poseof the best docking pose.
f)

35
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

10. Summary, Additional Resources, and References
In this lesson, we imported and prepared a protein and ligand file, then visualized andanalyzed the protein-ligand complex. A raw PDB file was made suitable for modelingpurposes using the Protein Preparation Workflow, and the cognate ligand was
extrapolated using LigPrep in the same fashion that would be used for a multi-ligand
file. Then the prepared ligand was docked into the prepared protein using Glide. The
Workspace Configuration toolbar allowed for toggling various components in theWorkspace and the 2D view in the Ligand Interaction Diagram gave another way toanalyze information.
For further information, please see:
Maestro 11 Training Portal
Protein Preparation Workflow Panel Help
Glossary of Terms:
cognate ligand - a ligand that is bound to its protein target
Entry List - a simplified view of the Project Table that allows you to perform basic
operations such as selection and inclusion
included - the entry is represented in the Workspace, the circle in the In column is blue
incorporated - once a job is finished, output files from the Working Directory are added
to the project and shown in the Entry List and Project Table
Project Table - displays the contents of a project and is also an interface for performing
operations on selected entries, viewing properties, and organizing structures and data
Scratch Project - a temporary project in which work is not saved, closing a scratch
project removes all current work and begins a new scratch project
selected - (1) the atoms are chosen in the Workspace. These atoms are referred to as"the selection" or "the atom selection". Workspace operations are performed on theselected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row
for the entry is highlighted. Project operations are performed on all selected entries
Working Directory - the location that files are saved
36
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.

Workspace - the 3D display area in the center of the main window, where molecular
structures are displayed

37
The recipient shall not use the Schrödinger software, materials and information other than for the purposes for which they were distributed. Schrödinger owns the software and all materials, and retains all related
intellectual property rights. Schrödinger will retain all intellectual property rights relating to any suggestions, ideas, enhancement requests, feedback, recommendations or other information provided by therecipient or any third party. The recipient shall not use Schrödinger’s names or marks without Schrödinger’s prior written consent. THE SOFTWARE AND MATERIALS ARE PROVIDED "AS IS" WITHOUTWARRANTY OF ANY KIND. TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL SCHRÖDINGER OR ITS AFFILIATES OR LICENSORS BE LIABLE FOR ANY SPECIAL,INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES.