2022-1

Building Homology Models with

the Multiple Sequence
Viewer/Editor
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 Building Homology Models with the Multiple
Sequence Viewer/Editor

Created with: Release 2021-4

Required Files: FXa_homologymodeling.prjzip, factorXa_human.fasta

Keywords: model assessment, model refinement, protein structure quality

viewer

BioLuminate can quickly build a homology model of the human protein factor Xa using sequence
information as a template.

Words found in the Glossary of Terms are shown like this: Workspace
File names are shown with the extension like this: 1fjs.pdb
Items that you click or type are shown like this: File > Import Structures

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

This tutorial consists of the following sections:

1. Creating Projects and Importing Structures

2. Building a Model and Assessing Quality

3. Refining a Model

4. Conclusion and References

5. Glossary of Terms
1. Creating Projects and Importing Structures
At the start of the session, change the file path to your chosen Working Directory in Maestro to make
file navigation easier. Each session in Maestro begins with a default Scratch Project, which is not
saved. A Maestro project stores all your data and has a .prj extension. A project may contain
numerous entries corresponding to imported structures, as well as the output of modeling-related
tasks. Once a project is created, the project is automatically saved each time a change is made.

Structures can be imported from the PDB directly, or from your Working Directory using File > Import
Structures, and are added to the Entry List and Project Table. The Entry List is located to the left of
the Workspace. The Project Table can be accessed by Ctrl+T (Cmd+T) or Window > Project Table
if you would like to see an expanded view of your project data. The Toggle Table is another way to
interact with structures and can be accessed via Window > Toggle Table.

1. Double-click the BioLuminate icon

○ (No icon? See Starting Maestro)

2. Go to File > Change Working Directory

3. Find your directory, and click Choose
4. Pre-generated input and results files are
included for running jobs or examining
output. Download the zip file here:
content.schrodinger.com/tutorials_zipfile/
2022-1/hm_msv.zip
5. After downloading the zip file, unzip the
contents in your Working Directory for
ease of access throughout the tutorial

Figure 1-1. Change Working Directory option.

6. Go to File > Open Project

7. Choose
FXa_homologymodeling.prjzip
8. Click Open
○ Structures are shown in the Entry
List
○ A structure is included in the
Workspace
12. In the Save scratch project warning box,
click OK
Figure 1-2. Open Project.
 13. Go to File > Save Project As
14. Change the File name to
MSV_homology
15. Click Save
○ The project is now named
MSV_homology.prj

Note: Please see the Glossary of Terms for the

distinction between included and selected

Figure 1-3. Save Project.

2. Building a Model and Assessing Quality

Sometimes structure-based drug design projects lack a suitable 3D structure of the protein of interest
and only the primary sequence information is available. Homology modeling can be used to build a
3D model using a suitable homolog, or homologs, which act as a structural template for the sequence.
Homology modeling works on the premise that sequence similarity can equate to structural similarity.

2.1 Build a homology model

1. Go to Tasks > Biologics > Multiple
Sequence Viewer/Editor
○ The Multiple Sequence
Viewer/Editor panel opens

Figure 2-1. Multiple Sequence Viewer/Editor

option in Biologics Tasks.
 2. Go to File > Import Sequences from
File
3. Choose factorXa_human.fasta and
click Open
4. Click Other Task and choose Build
Homology Model
○ The Build Homology panel opens

Figure 2-2. The Multiple Sequence Viewer/Editor

panel.

5. For Find a Template Structure, click Find

○ A dialog appears
6. Click the cog
7. Uncheck Use local server only

Note: This requires internet access

8. Click Run Search

Figure 2-3. Find Homologs.

9. In the BLAST Search Results panel,

choose 1KIG_H
10. Click Import

Figure 2-4. BLAST Search Results panel with

1K1G_H chosen.
 Note: The auto-align of the sequences when the
template was imported was sufficient, so we do
not need to proceed with any further alignment

11. For Job name write

homology_modeling_FXa
12. Click Generate Model
○ The job should take a few minutes
○ Once completed, a new entry is
added to the Entry List

Figure 2-5. Run the Homology Model job.

Note: Output structure annotated by color

● Blue - full residue conformation is copied
from the template, identical residues are
at this position
● Cyan - residue backbone conformation is
copied from the template, a sidechain
mutation is at this position
● Red - residue backbone and sidechain
positions have been modeled, an
insertion, deletion, or experimental
constraint requires this position to be
predicted
Figure 2-6. The homology model annotated by
color.
2.2 Assess model quality
1. Go to Tasks > Biologics > Structure
Reliability Report
○ The Protein Reliability Report
opens

Figure 2-7. Structure Reliability Report in

Biologics

2. Change job name to

homology_reliability
3. Click Run
○ This step takes ~2 minutes
○ A new entry is added to the Entry
List
○ A banner appears

Figure 2-8. Protein Reliability Report panel.

4. On the banner, click Protein Reliability

Report
○ The Protein Reliability Report
Panel Opens

Note: The Protein Reliability Report output can

also be viewed by including
homology_reliability-out in the Workspace and
reopening the Protein Reliability Report Panel
through Tasks > Biologics > Reliability Report

Note: In the Protein Reliability Report, small

green circles represent properties within a
reasonable distance of the average PDB
structure, while large red circles are considered
 Figure 2-9. The Protein Report tab of the Protein potential matters of concern. In general, the
Structure Quality Viewer showing Steric three outputs that are looked at to determine
Clashes. the quality of a protein structure are ‘Steric
Clashes’, ‘Missing Atoms’ and ‘Missing Loops’

Note: Click on any of the circles for a more in-

depth analysis

3. Refining a Model
After building a model, you can examine its quality and fix problems, such as steric clashes, prior to
using the model for further calculations. Two tools for refining structures are the Protein Preparation
Workflow and Prime Loop Refinement. Most common structural problems can be resolved using the
Protein Preparation Workflow, while Prime Loop Refinement can address more complex issues. Prime
Loop Refinement is a time and CPU-intensive calculation, so the Protein Preparation Workflow is the
recommended starting point for model refinement. Please see the Introduction to Structure
Preparation and Visualization tutorial for more details on using the Protein Preparation Workflow.

1. In the Favorites Bar, Click Protein

Preparation
○ The Protein Preparation Workflow
panel opens
2. Click INTERACTIVE
3. Under Optimize H-bond Assignments,
click Optimize
○ This step takes about a minute
○ A new entry is in the Entry List
○ The overlapping atoms have been
corrected, and side chains that
have been flipped are now labeled
Figure 3-1. The Refine tab of the Protein in the Workspace
Preparation Wizard. 4. Under Minimize and Delete Water, click
Clean Up
○ This step takes about a minute
○ A new entry is added to the Entry
List

Note: Hover over buttons to find out more about

their function
 5. In the Protein Reliability Report, change
job name
homology_reliability_prepared
6. Click Run
○ This step takes ~2 minutes
○ A new entry is added to the Entry
List
○ A banner appears
7. On the banner, click Protein Reliability
Report
○ The Protein Reliability Report
Panel Opens
Figure 3-2. Examine Protein Reliability Report
results. Note: There are large improvements in Steric
Clashes and Bond Angle Deviations compared
to the previous results.

4. Conclusion and References

This short tutorial explored the building homology models using the Multiple Sequence Viewer/Editor.
We built a homology model of the human Factor Xa using 1KIG, a bovine ortholog, as the template.
We assessed the quality of the model by generating a Structure Reliability Report. Finally, we used
the Protein Preparation Workflow to refine the structure and fix problems that were associated with
the model.
For further information, please see:
BioLuminate User Manual
Introduction to Structure Preparation and Visualization
Batch Homology Modeling Using the Multiple Sequence Viewer/Editor
Chimeric Homology Modeling Using the Multiple Sequence Viewer/Editor

5. Glossary of Terms
BLAST - Basic Local Alignment Search Tool, used for calculating sequence similarity

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 the selected 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

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