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Prevent firewall issues when downloading from the Motion Library
Miscellaneous Tasks » Prevent firewall issues when downloading from the Motion Library
When attempting to download files from the Motion Library on Windows, you may receive the following error message: I/O error when communicating with DNASTAR Motion Library Server. This issue may occur if Windows Firewall is On and Outbound Connections are Blocked.…
Open a structure from the Motion Library
Open a File or Project » Open a structure from the Motion Library
To open a structure from Protean 3D’s Motion Library: Open the Motion Library using any of these methods: Using the File > Open From Motion Library command Using the View > Motion Library command Pressing Ctrl+Alt+L (Windows) or Option+Cmd+L…
Motion Library
Protean 3D Interface » Motion Library
The Motion Library consists of over 500 animated and annotated macromolecular motions illustrating structural conformational changes. The intermediate structures in the animation are an interpolation between two experimentally-determined protein conformations…
Try it! – Open a multi-model file from the Motion Library
Protean 3D Interface » Motion Library » Try it! – Open a multi-model file from the Motion Library
This tutorial shows how to open and work with a multi-model file from the Motion Library. Choose File > Open from Motion Library to open the floating Motion Library window. In the Find area, enter isocitrate and click Search. One match will be shown. Notice…
Open a PDB file when you know the ID
Open a File or Project » Open a PDB file when you know the ID
To open a PDB file when you know the ID: Choose File > Open from PDB or press Ctrl/Cmd+D. For an additional shortcut to this command, see The Welcome Screen. Type a valid 4-digit ID in the text box. All PDB IDs consist of a single-digit number followed…
Open a structure from the NovaFold Report
Protean 3D Interface » Views » Report view » NovaFold report » Open a structure from the NovaFold Report
There are several links in the NovaFold Report that allow you to open a model as a new Protean 3D document. When opened, each selected model will appear as a .pdb-formatted structure in a separate tab of the Protean 3D window. The following table describes the…
Open a structure from the NovaDock Report
Protean 3D Interface » Views » Report view » NovaDock report » Open a structure from the NovaDock Report
There are several links in the NovaDock Report that allow you to open a model as a new Protean 3D document. When opened, each selected model will appear as a .pdb-formatted structure in a separate tab of the Protean 3D window. The following table describes the…
Export data from the Text, Table or Pairwise views
Save and Export » Export data from the Text, Table or Pairwise views
The Export data tool ( ), located in the header above the Text, Table or Pairwise views, lets you export data from those views. This tool provides a choice of three options, one of which has four sub-options. Options include: Export Data > Matches…
Export a table of results from the Analysis view
Save and Export » Export a table of results from the Analysis view
To export a table showing results from all methods currently applied to the Analysis view, use File > Export Data > Export Analysis Data. Choose the Save as type; either tab-separated values (.tsv) or comma-separated values (.csv). The .tsv file type is designed to be…
Open a PDB file when you don’t know the ID
Open a File or Project » Open a PDB file when you don’t know the ID
Protein structure files are available for free download via the RCSB Protein Data Bank. If you don’t know the 4-digit PDB ID for a structure, you can locate the structure on the PDB website, and then download it to use later in Protean 3D. Alternatively, you…
Try it! – Make a selection from the Sequence view
Make a Selection » Try it! – Make a selection from the Sequence view
In this tutorial, you will learn how to make a selection from the Structure and Sequence views. You will also confirm that the same selection appears in other views. Within Protean 3D, choose File > Open from PDB. You may initially see a yellow warning icon ()…
When no document or a blank document is open
Protean 3D Interface » Panels » Details panel » When no document or a blank document is open
When no document or a blank document is open, the Details panel displays information for getting started in Protean 3D. Click on the links to: Open a file Open a structure from the PDB Open the Motion Library Start a new NovaCloud prediction Start a new…
The NovaFold report
Protean 3D Interface » Panels » Details panel » The NovaFold report
For most selections made in the NovaFold report, the Details panel provides the information shown in the table below. Title The molecule name. Summary Residues - Number of residues in the sequence. Started - Date…
The NovaDock report
Protean 3D Interface » Panels » Details panel » The NovaDock report
The Details panel is the only panel enabled when viewing the NovaDock report. This panel contains expandable areas that can be displayed or hidden by clicking the small blue triangle in its header. Title The name of the NovaDock file. …
Uninstall the software
Predict Structures, Antibody Interactions and Docking » Run Nova applications locally » Install and set up the software » Uninstall the software
To remove a Nova application: If you want to remove one of the Nova applications, use either of these commands: # /opt/dnastar//uninstall $ sudo/opt/dnastar//uninstall Note that removal requires root access or elevated (sudo) privileges. If there are multiple…
Reinstall the software
Predict Structures, Antibody Interactions and Docking » Run Nova applications locally » Install and set up the software » Reinstall the software
If you have installed the Nova applications successfully in the past, subsequent reinstallation may result in one or more error messages. Simple steps for resolving these errors are described below: Error: failed to remove one or more images This issue occurs when…
Part B: Compare results from two tracks
Protean 3D Interface » Views » Analysis view » Try it! – Apply tracks to the Analysis view » Part B: Compare results from two tracks
This part of the tutorial follows Part A: Apply and reorder tracks. Part B demonstrates how the results of one track can be corroborated by looking at a similar graph from another track. So far, only the synopsis row for each track is visible in the Analysis view. …
Change the default print size
Miscellaneous Tasks » Change the default print size
Unless otherwise specified on your computer, the default printing size for all DNASTAR applications is “U.S. Letter” size (8.5 × 11 inches = 21.6 × 28 cm). You can temporarily change to another size, such as A4, from within the application. However, the…
Prepare the input file(s)
Predict Structures, Antibody Interactions and Docking » Run Nova applications locally » Prepare the input file(s)
Application Directory contents NovaFold A FASTA-format protein sequence file containing a single sequence or chain. Maximum sequence length is 2,000 residues. NovaFold Antibody A FASTA-format protein sequence file…
Colors in the Analysis view
Protean 3D Interface » Views » Analysis view » Colors in the Analysis view
Default colors in the Analysis view are assigned by track classification and channel type:
Customize the Look and Layout
Customize the Look and Layout
The following topics describe the many ways you can customize the look and layout of Protean 3D. Use the Style panel to change the look of a view (font styles and sizes, colors, number of decimal places, etc.) Customize the appearance and layout of…
Miscellaneous Tasks
Miscellaneous Tasks
The following topics cover tasks and troubleshooting tips that do not fit into any of the main help categories: General tasks Troubleshooting Use basic editing commands Set preferences Synchronize sequence updates between two Lasergene…
Install and set up the software
Predict Structures, Antibody Interactions and Docking » Run Nova applications locally » Install and set up the software
Before installing NovaFold, NovaFold Antibody, or NovaDock for local use, you must first install Docker, a computing platform for distributed applications that is needed to run the programs. On a Windows or Macintosh computer: Download and install the DNASTAR License…
Update the PROSITE database between releases
Protean 3D Interface » Panels » Tracks panel » Track Options section » Database tracks » Domains & Sites (PROSITE) » Update the PROSITE database between releases
You may update the PROSITE database at any time following the steps below: Go to this ExPASy web page, then select the Downloads tab from the top of the page. From the ftp directory, right-click on the file prosite.dat and select Save Link As. In the…
Change the default application for opening files
Open a File or Project » Open one or more local files » Change the default application for opening files
Windows 7 and Windows 8: Open the Control Panel. Go to Programs > Default Programs > Associate a file type or protocol with a specific program. Select extension you wish to change in the Extensions list and then click the Change program button. Click the…
Run Nova applications through the DNASTAR website
Predict Structures, Antibody Interactions and Docking » Run Nova applications through the DNASTAR website
This topic is a general overview on how to set up, run and view NovaFold, NovaFold Antibody and NovaDock through the DNASTAR website. If you are instead running these services through the Protean 3D interface, see “Run NovaFold / NovaFold Antibody / NovaDock…
Customize the layout of other window components
Customize the Look and Layout » Customize the layout of other window components
Controls for this application’s view, panels and expand bars are described in the following table. For information that pertains only to views, also see Customize the appearance and layout of views. Task “How To” Show or open a hidden…
Customize the appearance and layout of views
Customize the Look and Layout » Customize the appearance and layout of views
The following table lists ways in which you can customize the appearance and layout of views. Task How to… To show a view Use View > (View Name) > Show. To detach the view Use View > (View Name) > Detach or right-click…
Try it! – Use the Structure view toolbar
Protean 3D Interface » Views » Structure view » Try it! – Use the Structure view toolbar
This tutorial provides practice using the toolbar from within the Structure view. Within Protean 3D, choose File > Open from PDB. You may initially see a yellow warning icon () prompting you to type in a valid ID. Type 7TIM into the text box. Press OK to…
Default colors and styles in the Structure view
Protean 3D Interface » Views » Structure view » Default colors and styles in the Structure view
The tables below shows the default colors and styles of various entities in the Structure view. To select a different color for a selection or a different set of colors for the entire molecule, use the Color section of the Style panel. To select a different…
Run Nova applications within the Protean 3D interface
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface
Click the links below to learn how to run the various Nova applications from within the Protean 3D interface: NovaFold NovaFold AI NovaFold Antibody NovaDock
Part D: View the protein structure in Protean 3D
Evaluate Variants Produced in a SeqMan NGen Assembly » Part D: View the protein structure in Protean 3D
After finishing Part C, the protein structure with the variant of interest opens in Protean 3D. In the Molecules section, two near-identical copies of the structure appear. The upper structure is the original structure from the Protein Data Bank (PDB). The lower…
Try it! – Apply tracks to the Analysis view
Protean 3D Interface » Views » Analysis view » Try it! – Apply tracks to the Analysis view
Protean 3D’s Analysis View allows you to apply a variety of prediction tracks to your protein sequence. In this four-part tutorial, you will locate potential calcium-binding regions for a human calmodulin sequence. We know from the literature that these regions are…
Try it! – Change the rendering of a structure
Protean 3D Interface » Panels » Style panel » Rendering section » Try it! – Change the rendering of a structure
Within Protean 3D, choose File > Open from PDB. You may initially see a yellow warning icon () prompting you to type in a valid ID. Type 7TIM into the text box. Press OK to open the structure in Protean 3D. Go to the Style panel bar and expand the…
Save the layout and apply it to other projects
Customize the Look and Layout » Save the layout and apply it to other projects
You can change the layout of Protean 3D’s views and panels as described in Customize the look and layout. Once you have arrived at a layout you like, you can save it and then apply it to future projects, either by default or only when you specify that it be…
Troubleshoot the error “A different version is running”
Miscellaneous Tasks » Troubleshoot the error “A different version is running”
If you receive the error “A different version of Lasergene is running” when you try to launch a Lasergene application, but another version of Lasergene actually isn’t running, there may be a lingering .state file from another version that needs to be…
Try it! – Use the Molecules section to select and hide a structural element
Protean 3D Interface » Panels » Explorer panel » Molecules section » Try it! – Use the Molecules section to select and hide a structural element
This tutorial shows how to select a particular structural element from the Molecules section. Within Protean 3D, choose File > Open from PDB. You may initially see a yellow warning icon () prompting you to type in a valid ID. Type 7TIM into the text box. …
Open a File or Project
Open a File or Project
The following topics discuss different ways of opening structure files, protein sequence files, or saved Protean 3D projects; Open one or more local files (protein sequences, structures, or NovaCloud results files) (Change the default application for opening…
Welcome screen
Protean 3D Interface » Welcome screen
The Welcome “project” opens when you launch Protean 3D and is a central location for opening protein projects, searching NCBI databases, getting help, and much more. As you add projects, the Welcome “project” will remain as the leftmost tab…
Protean 3D Tutorials
Protean 3D Tutorials
In this User Guide, tutorial topics are located in the table of contents directly below the corresponding help topic. To help you find the tutorials, they are also listed below. Use the Structure view toolbar (Structure view) Apply tracks to the Analysis view…
Protean 3D Interface
Protean 3D Interface
Protean 3D’s views, panels and tabs (pictured and described below) can be resized and/or undocked and moved anywhere inside or outside the Protean 3D application window. Changes and selections are synchronized between all views. Item Description…
Protein Design wizard: Options
Create or Find Variants using Protein Design » Protein Design wizard: Options
Options is the fourth screen of the Protein Design wizard. Enter the substitution variations you wish to model. Repack neighbors – When this box is checked, as it is by default, the residues in contact with the variant positions are also repacked during…
NovaDock wizard: Options
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Run NovaDock through Protean 3D » NovaDock wizard: Options
When you predict protein docking with NovaDock, the second wizard screen is Options. This screen allows you to edit or specify prediction options. During the prediction step, options specified in this screen are applied to all docking jobs listed in the Structures…
Useful links
Appendix » Useful links
Name and Link Description CATH Protein Structure Classification Database A curated classification of protein domain structures. Each protein is assigned to a homologous superfamily (group of domains related by evolution). The CATH…
Welcome to Protean 3D
Welcome to Protean 3D
Protean 3D is Lasergene’s application for exploring macromolecular structure, motion, and function. Rich, synchronized graphical views allow you to see the 3D molecular structure, the annotated sequence, and the analysis of applied prediction methods…
Export an animation or video
Save and Export » Export an animation or video
To save an animated sequence in QuickTime Movie (.mov) or .avi format, choose File > Export Movie. Both formats are saved to play back at 6 frames per second (166 ms/frame), which is one-quarter the speed of standard television programs and films. This speed was…
Glossary
Appendix » Glossary
Most of the definitions in the table below are courtesy of the PDB Glossary of Technical Terms. Term Definition Active site, binding site, or site The region of a protein that binds substrates and that is involved in chemical reactions.…
Optional arguments
Predict Structures, Antibody Interactions and Docking » Run Nova applications locally » Set up and run a prediction » Optional arguments
The following table shows optional arguments when scripting a local Nova application prediction. Only a subset of these arguments is available, depending on the application. The three rightmost columns show whether the argument applies to NF (NovaFold), NFA (NovaFold…
Save a document
Save and Export » Save a document
To save a new document in the .structure format, or to overwrite a previously saved version of the document, choose File > Save, or use Ctrl+S (Win) or Cmd+S (Mac). If you want to preserve the earlier version of a .structure document, or store a copy of the…
NovaFold Antibody wizard: Options
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Run NovaFold Antibody through Protean 3D » NovaFold Antibody wizard: Options
When you predict antibody interactions with NovaFold Antibody, the second wizard screen is Options. During the prediction step, options specified in this screen are applied to all jobs listed in the Sequences screen. Edit or enter information in this wizard screen…
NovaDock: protein-protein docking
Predict Structures, Antibody Interactions and Docking » Types of predictions » NovaDock: protein-protein docking
NovaDock is DNASTAR’s protein docking application. DNASTAR provides NovaDock as a local or cloud-based, separately licensed service within Protean 3D. NovaDock’s algorithm is based on SwarmDock, developed in Dr. Paul Bates’ laboratory at the Cancer…
Sequence view
Protean 3D Interface » Views » Sequence view
The Sequence view displays the amino acid or nucleotide sequence, secondary structures, binding sites, disulfide bonds, and a ruler. Colorful graphics denote features derived from annotations in the structure file. By default, the Sequence view is shown vertically in…
NovaFold Report: Model Overview
Protean 3D Interface » Views » Report view » NovaFold report » NovaFold Report: Model Overview
The Model Overview section of the NovaFold Report allows you compare the structural similarity of a NovaFold prediction to experimental structures in the RCSB Protein Data Bank (PDB). Model – The model ID number. TM-score - Template modeling…
Supplemental arguments
Predict Structures, Antibody Interactions and Docking » Run Nova applications locally » Set up and run a prediction » Supplemental arguments
The following table shows supplemental arguments when scripting a local Nova application prediction. Only a subset of these arguments is available, depending on the application. The three rightmost columns show whether the argument applies to NF (NovaFold), NFA…
Research references
Appendix » Research references
Chou PY (1990). "Prediction of protein structural classes from amino acid composition." In Prediction of Protein Structure and the Principles of Protein Conformation, Plenum Press, New York, NY, pp. 549-586. Chou PY and Fasman GD (1978). "Prediction of the…
Analysis view
Protean 3D Interface » Views » Analysis view
The Analysis view lets you quickly find regions of interest on a protein sequence. By default, the Analysis view is shown in the bottom left of the Protean 3D window. If the Analysis view is hidden or absent, you can display it using View > Analysis > Show.…
NovaCloud Services view
Protean 3D Interface » Views » NovaCloud Services view
NovaCloud Services allows you to make a prediction using NovaFold, NovaFold AI, NovaFold Antibody, or NovaDock. Open the Services view using any of the following menu commands or keyboard shortcuts. Note that some commands are only available if a protein sequence…
Try it! – Use NovaFold to predict a protein structure
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Run NovaFold through Protean 3D » Try it! – Use NovaFold to predict a protein structure
The following tutorial is separated into four parts for clarity, but the entire tutorial only requires about 15 minutes of “hands-on” time. Between Parts A & B, there is also a 12-24 hour wait for the prediction to take place. Part A: Use NovaFold to…
NovaFold report
Protean 3D Interface » Views » Report view » NovaFold report
When you open a completed NovaFold prediction (.novafold) in Protean 3D, a specialized Report view contains detailed results about the prediction. The sections of the NovaFold Report are: Molecule Templates Model Overview Model ‘x’ and its…
Set data preferences
Miscellaneous Tasks » Set preferences » Set data preferences
The Data Preferences dialog designates the folder in which PDB data files are stored when using the File > Open from PDB command. By default, PDB files are downloaded to the \Protean3D\Temp\Cache\PDB folder. On Windows, this dialog is accessed via the command Edit >…
(Feature) Style section
Protean 3D Interface » Panels » Features panel » (Feature) Style section
The Style section is located in the Features panel and provides options for customizing the look of features in the Analysis view. Opening the Style section: Do either of the following: Click the expand bar entitled “Features” Use View > Style > Style The…
NovaDock report
Protean 3D Interface » Views » Report view » NovaDock report
When you open a completed NovaDock prediction (.novadock) in Protean 3D, a specialized Report view contains detailed results about the prediction. The sections of the NovaDock Report are: Molecules Model Overview Model and its subsection: Models in…
Part B: Translation in SeqNinja
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Try it! – Phage display assembly, translation and prediction » Part B: Translation in SeqNinja
In this part of the tutorial, you will use SeqNinja to batch translate the sequences. Launch SeqNinja and choose Translate from the menu on the right. Navigate to and open the Exported Sequences.gbk file. The Choose Translation Options dialog appears. …
Overlay One Structure on Another
Overlay One Structure on Another
To overlay a structure on an already-open structure: Open the first structure file. Choose File > Add to Document or press Ctrl/Cmd+E. In the ensuing dialog, choose the placement of the structure(s): To place the center of one structure directly on…
Set Internet preferences
Miscellaneous Tasks » Set preferences » Set Internet preferences
The Internet Preferences dialog lets you choose whether you wish to be notified about Lasergene updates. On Windows, this dialog is accessed via the command Edit > Preferences. On Macintosh, it is accessed using Protean 3D > Preferences (macOS 12 and lower) or Protean…
Features (Annotated) tracks
Protean 3D Interface » Panels » Tracks panel » Track Options section » Features (Annotated) tracks
In the Analysis view, you can display selected features from the protein sequence file on the same axis with the prediction tracks. PDB files contain sites, disulfide bonds, helices, and sheets/strands, while Lasergene and Genbank files support many more feature types,…
Stability – Isoelectric Precipitate
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Stability – Isoelectric Precipitate
The Stability – Isoelectric Precipitate track predicts regional instability by identifying uncharged regions at a given pH, which have an increased potential to aggregate if surface exposed. This method uses the pKa tables from Lehninger et al., 2005. To apply…
Molecules section
Protean 3D Interface » Panels » Explorer panel » Molecules section
The Molecules section is located in the Explorer panel lists the structures and components (chains, ligands and water) for each structure in the current document. If you display/hide/select items in the Molecules section, these choices are simultaneously…
Try it! – Align multiple structures using jFATCAT
Align Multiple Structures » Try it! – Align multiple structures using jFATCAT
This tutorial demonstrates how to align two structurally homologous protein files within a single document. This technique is useful for discovering similarities and differences between related structures. The files used in this tutorial will be opened from the RCSB…
(Feature) Options section
Protean 3D Interface » Panels » Features panel » (Feature) Options section
The Options section is located in the Features panel and, in some circumstances, lets you edit the bounds of secondary structure elements and/or change their descriptions. Opening the Options section: Do either of the following: Click the expand bar entitled…
Export a structure file
Save and Export » Export a structure file
To export the selected portion of a currently-displayed structure (or entire structure, if nothing is selected), choose one of the following File > Export Data options: Export Structure – Available for documents with one structure. By default, the…
Part D: Structure prediction and docking in Protean 3D
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Try it! – Phage display assembly, translation and prediction » Part D: Structure prediction and docking in Protean 3D
In this portion of the tutorial, you will use Protean 3D and the NovaApps to create a homology model of the sequence and simulate docking of the predicted antibody structures to the target epitope. Launch Protean 3D and click the Structure Prediction tab on the…
Color section
Protean 3D Interface » Panels » Style panel » Color section
The Color section, located in the Style panel, lets you adjust colors of selected components of the Structure view or of that view’s background. Opening the Color section: Do either of the following: Click the expand bar entitled Color Use View > Style >…
NovaDock Report: Molecules
Protean 3D Interface » Views » Report view » NovaDock report » NovaDock Report: Molecules
The Molecules section of the NovaDock Report displays information about the receptor and ligand structures that were used as inputs in the NovaDock prediction. To view or hide this section of the report, click on the expand arrow (small blue triangle) in its header. …
Work with Features
Work with Features
The following video is a brief introduction to working with features in Protean 3D: For detailed information, see the table below: Task How To To control which features are displayed in the Sequence and Analysis views See Features panel.…
Transmembrane – von Heijne
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Transmembrane – von Heijne
The Transmembrane – von Heijne track predicts hydropathy based on the interaction between the signal sequence and membrane, using the approach of von Heijne et al., 1981. The Transmembrane – von Heijne method is similar to Goldman-Engleman-Steitz, another…
Surfaces section
Protean 3D Interface » Panels » Explorer panel » Surfaces section
The Surfaces section is located in the Explorer panel and is used to create molecular or solvent-accessible surfaces for selections in the Structure view. The following video shows the Surfaces section in action: Opening the Surfaces section: Do any of the…
Protein Design reports (Variants and Hot Spot Scan)
Protean 3D Interface » Views » Report view » Protein Design reports (Variants and Hot Spot Scan)
The Protein Design reports, “Variants” and “Hot Spot Scan,” are two similar versions of the Report view. Both versions contain data that can be used to predict whether a SNP might be stabilizing or destabilizing to a protein structure. These…
Predicted Binding Sites
Protean 3D Interface » Views » Report view » NovaFold report » NovaFold Report: Model » Predicted Binding Sites
If you checked Predict ligand binding sites and protein function in the NovaFold Options screen, the Predicted Binding Sites section of the NovaFold Report is available for Model 1, and for any model with a predicted TM-score ≥ 0.5. This section lists predicted…
NovaFold wizard: Sequences
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Run NovaFold through Protean 3D » NovaFold wizard: Sequences
When setting up a NovaFold prediction in Protean 3D’s NovaFold wizard, the first screen is Sequences. This screen is used to specify the protein sequence(s) to use for the prediction(s). The number of sequences you can enter/upload to submit for folding depends…
NovaDock wizard: Structures
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Run NovaDock through Protean 3D » NovaDock wizard: Structures
When you predict protein docking with NovaDock, the first wizard screen is Structures. This screen prompts you to specify structure files to use as the receptor and as the ligand(s) in a docking simulation. The number of predictions you can submit for folding depends…
Predicted Enzyme Function
Protean 3D Interface » Views » Report view » NovaFold report » NovaFold Report: Model » Predicted Enzyme Function
If you checked Predict ligand binding sites and protein function in the NovaFold Options screen, the Predicted Enzyme Function section of the NovaFold Report is available for Model 1, and for any model with a predicted TM-score ≥ 0.5. During calculation, NovaFold…
NovaFold AI wizard: Sequences
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Run NovaFold AI through Protean 3D » NovaFold AI wizard: Sequences
When you predict protein structure with NovaFold AI, the wizard begins with the Sequences screen. This screen is used to specify the protein sequence(s) to use for the prediction(s). The number of sequences you can enter/upload to submit for folding depends on the type…
NovaFold Antibody wizard: Sequences
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Run NovaFold Antibody through Protean 3D » NovaFold Antibody wizard: Sequences
When you predict antibody interactions with NovaFold Antibody, the wizard begins with the Sequences screen. This screen is used to specify the protein sequence(s) to use for the prediction(s). The number of sequences you can enter/upload to submit for folding depends…
Part C: Alignment in MegAlign Pro
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Try it! – Phage display assembly, translation and prediction » Part C: Alignment in MegAlign Pro
In this section of the tutorial, you will use MegAlign Pro to align sequences and create a phylogenetic tree. Launch MegAlign Pro and choose New blank alignment project. Use File > Add Sequences and add the Exported Sequences_translated.fasta file…
B-Cell Epitopes (DNASTAR)
Protean 3D Interface » Panels » Tracks panel » Track Options section » Immunogenicity tracks » B-Cell Epitopes (DNASTAR)
The B-Cell Epitopes (DNASTAR) prediction track uses a bioinformatics approach that uses experimental antibody recognition data. For a set of peptides provided by NeoClone® Biotechnology International, LLC (Madison, WI USA), the antigenicity of each peptide was…
Table view
Protean 3D Interface » Views » Table view
After the Jobs panel shows the Status of a BLAST search or Entrez search is Done, pressing the “Done” hyperlink opens the search results simultaneously in the Text, Table, and Pairwise views. All three views are contained in a large pop up window that is…
NovaFold Antibody: antibody interaction prediction
Predict Structures, Antibody Interactions and Docking » Types of predictions » NovaFold Antibody: antibody interaction prediction
NovaFold Antibody is specifically designed to generate models of antibodies and antibody fragments (Fv, Fab, VH, sdAb) and, with the use of NovaDock, predict the structure of antibody-antigen complexes. DNASTAR provides NovaFold Antibody as a local or cloud-based,…
NovaDock Report: Model Overview
Protean 3D Interface » Views » Report view » NovaDock report » NovaDock Report: Model Overview
This section of the NovaDock Report represents the top ten ligand-receptor docking models predicted by NovaDock. To view or hide this section of the report, click on the expand arrow (small blue triangle) in its header. The thumbnail preview image acts as an…
Try it! – Use NovaFold AI to predict a protein structure with a cytosolic domain
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Run NovaFold AI through Protean 3D » Try it! – Use NovaFold AI to predict a protein structure with a cytosolic domain
In this tutorial, you will download the protein sequence of an adhesion GPCR with cytosolic domains. These domains cannot be seen using x-ray crystallography but can be accurately predicted using NovaFold AI. The tutorial is separated into four parts for clarity, but…
Style panel
Protean 3D Interface » Panels » Style panel
The Style panel, represented by a palette icon (), includes four expandable sections that affect the appearance of the Structure and/or Sequence views. Opening the Style panel: Do any of the following: Click on the Style tab Choose View > Style Press…
A molecule, feature or region
Protean 3D Interface » Panels » Details panel » A molecule, feature or region
If the active selection consists of one or more molecules, features or regions, the Details panel contains the following information: Title The name or type of molecule, feature or region. If a region is selected, the text will read "Selected…
NovaFold AI wizard: Options
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Run NovaFold AI through Protean 3D » NovaFold AI wizard: Options
When you predict a protein structure with NovaFold AI, the second wizard screen is Options. During the prediction step, options specified in this screen are applied to all jobs listed in the Sequences screen. Edit or enter information in this wizard screen as…
Part B (optional): Filter for variants of interest in ArrayStar
Evaluate Variants Produced in a SeqMan NGen Assembly » Part B (optional): Filter for variants of interest in ArrayStar
This is continued from Part A: Create a templated assembly in SeqMan NGen. If your assembly has a large number of variants, you can use ArrayStar to filter them down to a smaller group of interest before sending them to SeqMan Pro for viewing. This optional step is…
Use a mouse or trackpad with Protean 3D
Miscellaneous Tasks » Use a mouse or trackpad with Protean 3D
Protean 3D’s user interface is controlled by a combination of menu commands, toolbar icon selections and mouse clicks. For best results, we recommend using a 3-button mouse with Protean 3D. However, single-button versions and trackpads are also…
Protein Design wizard: Substitutes
Create or Find Variants using Protein Design » Protein Design wizard: Substitutes
Substitutes is the third screen of the Protein Design wizard. When using certain menu commands, the wizard opens to this screen, already prepopulated with the currently-selected residues. Each row of the table represents a single residue. Chain – The…
Rendering section
Protean 3D Interface » Panels » Style panel » Rendering section
The Rendering section is located in the Style panel, and provides options for customizing the look of the Structure view. The following video is a brief walkthrough showing how to apply a different rendering style to highlight features of interest: Opening the…
Part A. Assembly and trimming in SeqMan Ultra
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Try it! – Phage display assembly, translation and prediction » Part A. Assembly and trimming in SeqMan Ultra
This section of the tutorial describes the procedure for working with .abi files, by far the most common file type used in this workflow. (NGS files are handled differently; please contact us for instructions.) In this section, you will use SeqMan Ultra to de novo…
NovaFold wizard: Options
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Run NovaFold through Protean 3D » NovaFold wizard: Options
When setting up a NovaFold prediction in Protean 3D’s NovaFold wizard, the second screen is Options. This screen allows you to edit or specify prediction options. During the prediction step, options specified in this screen are applied to all jobs listed in the…
Select neighboring residues
Create or Find Variants using Protein Design » Select neighboring residues
After creating or finding variants using Protein Design, a common situation is the desire to visualize the environment around the variant. You may want to know how the new sidechain fits in its environment, and whether or not it changes the rotamer of any other…