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User Guide to Protean 3D — 18.0
18.0
Table of Contents
Home Page
User Guide to Protean 3D — 18.0
User Guide to Protean 3D — 18.0
Welcome to Protean 3D
Separately-licensed services that integrate with Protean 3D
Protean 3D Tutorials
Protean 3D Interface
Welcome screen
Project tabs
Protean 3D toolbar
Views
Structure view
Try it! – Use the Structure view toolbar
Default colors and styles in the Structure view
Analysis view
Try it! – Apply tracks to the Analysis view
Part A: Apply and reorder tracks
Part B: Compare results from two tracks
Part C: Edit track options
Part D: Recolor tracks
Colors in the Analysis view
Sequence view
Report view
Composition report
Try it! – Study surface-exposed cysteines
Biophysical Properties report
Protein Design reports (Variants and Hot Spot Scan)
Filter hot spot scan results
NovaFold report
NovaFold Report: Molecule
NovaFold Report: Templates
NovaFold Report: Model Overview
NovaFold Report: Model
Similar Experimental Structures
Predicted Binding Sites
Predicted Enzyme Function
Predicted Protein Function
Open a structure from the NovaFold Report
NovaDock report
NovaDock Report: Molecules
NovaDock Report: Model Overview
NovaDock Report: Model
NovaDock Report: Models in Cluster
Open a structure from the NovaDock Report
NovaFold AI and NovaFold AI-Multimer Reports
Nova AI Report: Model Overview
Nova AI Report: Structural Alignment Report
NovaCloud Services view
Predictions view
Text view
Table view
Pairwise view
Fix issue with scrolling in the views (macOS only)
Panels
Explorer panel
Molecules section
Try it! – Use the Molecules section to select and hide a structural element
Surfaces section
Examples of surface types
Labels section
Features panel
Try it! – Select and recolor a feature, and change feature options
(Feature) Options section
(Feature) Style section
Tracks panel
Track Options section
Biophysics tracks
Amphiphilicity (Eisenberg)
Charge Density (Lehninger)
Disorder (JRONN)
Flexibility (Karplus-Schulz)
Hydropathy – Hopp-Woods
Hydropathy – Kyte-Doolittle
Hydropathy – Parker
Secondary Structure – Chou-Fasman
Secondary Structure – Deleage-Roux
Secondary Structure – Garnier-Robson
Secondary Structure – Coiled Coil
Stability – Aliphatic Index
Stability – Instability Index
Stability – Isoelectric Precipitate
Surface Probability (Emini)
Transmembrane – Goldman-Engleman-Steitz
Transmembrane – TopPred
Transmembrane – von Heijne
Immunogenicity tracks
Antigenicity – Jameson-Wolf
Antigenicity – Welling
B-Cell Epitopes (DNASTAR)
MHC II Epitopes (Sette)
T-Cell Epitopes – AMPHI
T-Cell Epitopes – Rothbard-Taylor
Database tracks
Cleavage Sites (Proteases)
List of proteases
Domains & Sites (PROSITE)
Update the PROSITE database between releases
Modifications (SUMOylation) track
NovaFold-related tracks
Features (Annotated) tracks
Details panel
When no document or a blank document is open
A single residue or ligand
A molecule, feature or region
An entire structure
Try it! – View details about a structure
A selected region or strand
A group of structures
A track
A protease pattern or profile
An individual protease match
A PROSITE pattern or profile
An individual PROSITE match
A Protein Design result
The NovaFold report
The NovaDock report
The NovaFold AI and NovaFold AI-Multimer report
Style panel
Rendering section
Try it! – Change the rendering of a structure
Examples of rendering styles
Color section
Sequence section
Lighting section
Models panel
Jobs panel
Motion Library
Try it! – Open a multi-model file from the Motion Library
Customize the Look and Layout
Customize the appearance and layout of views
Customize the layout of other window components
Save the layout and apply it to other projects
Open a File or Project
Open one or more local files
Change the default application for opening files
Type or paste a protein sequence
Open a PDB file when you know the ID
Open a PDB file when you don’t know the ID
Open a structure from the Motion Library
Open an existing Protean 3D project
Search for Sequence Matches
Set up local BLAST databases
Search for sequence matches using BLAST
Search wizard: Query
Search wizard: Search
Search wizard: Options
Search wizard: Job
Filter sequence search results
Search for text or accession number matches using Entrez
Filter text search results
Access ID dialog
Save and reopen saved search results
Align Multiple Structures
Try it! – Align multiple structures using jFATCAT
Make a Selection
Select neighboring residues
Try it! – Make a selection from the Sequence view
Work with Features
Overlay One Structure on Another
Create or Find Variants using Protein Design
Protein Design wizard: Workflow
Protein Design wizard: Structure
Protein Design wizard: Substitutes
Protein Design wizard: Options
Protein Design wizard: Job
View progress and see variant results
Use Protein Design for site-directed mutagenesis
Evaluate Variants Produced in a SeqMan NGen Assembly
Part A: Create a templated assembly in SeqMan NGen
Part B (optional): Filter for variants of interest in ArrayStar
Part C: View variants in SeqMan Pro
Part D: View the protein structure in Protean 3D
Predict Structures, Antibody Interactions and Docking
Types of predictions
NovaFold: protein structure prediction
NovaFold AI: protein structure prediction
NovaFold AI-Multimer: protein structure prediction for multimers
NovaFold Antibody: antibody interaction prediction
NovaDock: protein-protein docking
Run Nova applications within the Protean 3D interface
Run NovaFold through Protean 3D
NovaFold wizard: Sequences
NovaFold wizard: Options
NovaFold wizard: Submit
Try it! – Use NovaFold to predict a protein structure
Run NovaFold AI through Protean 3D
NovaFold AI wizard: Sequences
NovaFold AI wizard: Options
NovaFold AI wizard: Submit
Try it! – Use NovaFold AI to predict a protein structure with a cytosolic domain
Run NovaFold Antibody through Protean 3D
NovaFold Antibody wizard: Sequences
NovaFold Antibody wizard: Options
NovaFold Antibody wizard: Submit
Run NovaDock through Protean 3D
NovaDock wizard: Structures
NovaDock wizard: Options
NovaDock wizard: Submit
Run NovaFold AI-Multimer through Protean 3D
NovaFold AI-Multimer wizard: Sequences
NovaFold AI-Multimer wizard: Options
NovaFold AI-Multimer wizard: Submit
Try it! – Phage display assembly, translation and prediction
Part A. Assembly and trimming in SeqMan Ultra
Part B: Translation in SeqNinja
Part C: Alignment in MegAlign Pro
Part D: Structure prediction and docking in Protean 3D
Run Nova applications through the DNASTAR website
Run Nova applications locally
Install and set up the software
Uninstall the software
Reinstall the software
Prepare the input file(s)
Set up and run a prediction
Required commands
Required arguments
Optional arguments
Supplemental arguments
Stop a prediction in progress
Save and Export
Save a document
Export a still image
Export a structure file
Export a 3D model of the structure
Export an animation or video
Export data from the Text, Table or Pairwise views
Export a table of results from the Analysis view
Save or export a report
Close and Exit
Miscellaneous Tasks
Use basic editing commands
Set preferences
Set data preferences
Set Internet preferences
Set proteins preferences
Set temporary file preferences
Synchronize sequence updates between two Lasergene applications
Turn off usage logging
Use a mouse or trackpad with Protean 3D
Change the default print size
Prevent firewall issues when downloading from the Motion Library
Troubleshoot the error “A different version is running”
Troubleshoot blank Protean 3D window on Parallels Desktop
Appendix
Glossary
Supported file types
IUPAC codes
Installed Lasergene file locations
Useful links
Research references
Acknowledgements
Download as PDF
Appendix
Troubleshoot blank Protean 3D window on Parallels Desktop
Glossary
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