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Try it! – Study surface-exposed cysteines
Protean 3D Interface » Views » Report view » Composition report » Try it! – Study surface-exposed cysteines
Surface-exposed cysteine residues are of interest in industrial applications because they tend to form disulfide bridges with other molecules, disrupting the stability of the original protein. The following example shows one way to study cysteines in a protein…
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…
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…
Try it! – View details about a structure
Protean 3D Interface » Panels » Details panel » An entire structure » Try it! – View details about a structure
This tutorial demonstrates how to use the Details panel to view information about a structure or sequence. 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…
Try it! – Phage display assembly, translation and prediction
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Try it! – Phage display assembly, translation and prediction
Phage display panning is a tool used for the discovery of novel ligands against various targets of interest. In phage display panning, you will typically start with a batch of 96 _.abi. read files, each corresponding to one well of a 96-well ELISA assay. At the end of…
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…
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…
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 ()…
Try it! – Select and recolor a feature, and change feature options
Protean 3D Interface » Panels » Features panel » Try it! – Select and recolor a feature, and change feature options
In this tutorial, you will use the Features panel to select a feature to recolor. Next, you will edit some of the feature options. Within Protean 3D, choose File > Open from PDB. You may initially see a yellow warning icon () prompting you to type in a valid…
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…
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. …
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…
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…
Part D: Recolor tracks
Protean 3D Interface » Views » Analysis view » Try it! – Apply tracks to the Analysis view » Part D: Recolor tracks
This part of the tutorial follows Part C: Edit track options. In Part D, you will learn how to recolor a graph track in the Analysis view. Double-click on any green Alpha Regions graph to select it. If it is not already open, open the Color section by…
Open one or more local files
Open a File or Project » Open one or more local files
Protean 3D allows you to open a wide variety of supported file types, including protein sequences, structure files, and prediction results from the Nova applications. To open a single file within a Protean 3D project: Use the File > Open command, or press Ctrl+O…
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…
(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…
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…
Protein Design wizard: Workflow
Create or Find Variants using Protein Design » Protein Design wizard: Workflow
When using the commands File > New Protein Design Prediction or Modeling > Protein Design > New Protein Design Prediction, the Protein Design wizard opens at the Workflow screen. Choose one of the following workflows: Create specific variant – Allows the…
Use Protein Design for site-directed mutagenesis
Create or Find Variants using Protein Design » Use Protein Design for site-directed mutagenesis
Site-directed mutagenesis is a molecular biology method that is used to make specific changes to the DNA sequence of a gene. As of Lasergene 16.0, you can perform site-directed mutagenesis using Protean 3D’s Protein Design service together with SeqBuilder Pro.…
MHC II Epitopes (Sette)
Protean 3D Interface » Panels » Tracks panel » Track Options section » Immunogenicity tracks » MHC II Epitopes (Sette)
The MHC II Epitopes (Sette) track predicts peptide antigenic sites which interact with mouse MHC II haplotype d proteins. There are separate motifs for IAd and IEd haplotypes, and Sette et al., 1989, reports that this method finds more than 75% of known epitope sites…
Access ID dialog
Search for Sequences Online » Search for text or accession number matches (Entrez) » Access ID dialog
As of December 2018, NCBI requires an API key for faster access to NCBI services, or to run more searches concurrently. To get a key, start by setting up an NCBI account. After registering your account, click on your user name and request your key using API Key…
Structure view
Protean 3D Interface » Views » Structure view
The Structure view displays a physical representation of the molecule in your structure file. By default, the Structure view is shown in the upper left of the Protean 3D window. If the Structure view is hidden or absent, you can display it using View > Analysis > Show.…
Secondary Structure – Coiled Coil
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Secondary Structure – Coiled Coil
The Secondary Structure – Coiled Coil track predicts structures according to the formula of Lupas et al., 1991. You may use this track with the Transmembrane – Goldman-Engleman-Steitz track to predict transmembrane alpha helices. To apply this track to…
Select neighboring residues
Make a Selection » 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…
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…
Composition report
Protean 3D Interface » Views » Report view » Composition report
The Composition report is the default type of Report view for most situations. The Composition report table provides information about each individual amino acid, as well as amino acid categories. To open the Composition report, do either of the following: Use the…
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…
Part A: Apply and reorder tracks
Protean 3D Interface » Views » Analysis view » Try it! – Apply tracks to the Analysis view » Part A: Apply and reorder tracks
If you have not yet downloaded and extracted the tutorial data, click here to download it. Then decompress (unzip) the file archive using the method of your choice. In Protean 3D, use File > Open to open the protein sequence file Protean 3D Data/Human…
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…
Stop a prediction in progress
Predict Structures, Antibody Interactions and Docking » Run Nova applications locally » Set up and run a prediction » Stop a prediction in progress
Once you have set up and run a prediction, the process will normally stop running only after the prediction is finished. If you need to stop a prediction before it is complete: If you are in the terminal with the running process, press Ctrl+C to stop the…
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…
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…
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…
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.…
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 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…
Features panel
Protean 3D Interface » Panels » Features panel
The Features panel, represented by a “feature” icon (), shows the incidence of sequence features by type. This panel consists of an expandable tree listing all sites, disulfides (S-S bonds), helices, and sheets from the original PDB file, as well as Protean…
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…
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…
Synchronize sequence updates between two Lasergene applications
Miscellaneous Tasks » Synchronize sequence updates between two Lasergene applications
Synchronous updating allows you to work on the same file in multiple Lasergene applications at the same time, and is available in SeqBuilder Pro and GeneQuest, and—on a limited basis—in Protean 3D. Changes made to a sequence in one application are automatically…
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…
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…
Make a Selection
Make a Selection
Selections can be made from various views, panels and panel sections. Selections are synchronized between all views. To Select… Location Method A residue Structure View Double-click anywhere on the structure to select the…
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…
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,…
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…
Type or paste a protein sequence
Open a File or Project » Type or paste a protein sequence
To enter a protein sequence by pasting or typing text into a box: Do either of the following: Choose File > Enter Sequences. From the Welcome screen, click the Open Project tab and then the link Enter sequences. Following the model provided,…
NovaFold Report: Model
Protean 3D Interface » Views » Report view » NovaFold report » NovaFold Report: Model
For each model number in the NovaFold Report, there is an expandable report section featuring a mini Structure view with a rendering of the predicted structure. The scoring information at the top right reiterates data displayed in the Model Overview (see row…
Hydropathy – Kyte-Doolittle
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Hydropathy – Kyte-Doolittle
The Hydropathy – Kyte-Doolittle track predicts regional hydropathy of proteins from their amino acid sequences, using the approach of Kyte and Doolittle, 1982. Hydropathy values are assigned for all amino acids and are then averaged over a user-defined window. 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…
Search wizard: Options
Search for Sequences Online » Search for sequence matches (BLAST) » Search wizard: Options
The Options screen is the third of four screens in the BLAST Search wizard, and has two tabs: Selection and Matches. These tabs allow you to customize miscellaneous parameters relating to the BLAST search. Click the Selection tab to make it active. In the…
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…
Set temporary file preferences
Miscellaneous Tasks » Set preferences » Set temporary file preferences
Protean 3D creates and uses temporary files while a project is open. The need for temporary file space grows with the number and length of the sequences and amount of track data in open alignment projects. If you expect the temporary files will be too large to fit in…
Sequence section
Protean 3D Interface » Panels » Style panel » Sequence section
The Sequence section, located in the Style panel, allows you to change display characteristics of the Sequence view. Opening the Sequence section: Do either of the following: Click the expand bar entitled Sequence Use View > Style > Sequence *Note: The Sequence…
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 >…
Set proteins preferences
Miscellaneous Tasks » Set preferences » Set proteins preferences
The Proteins Preferences dialog lets you adjust how protein information is displayed. 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 3D > Settings…
Biophysical Properties report
Protean 3D Interface » Views » Report view » Biophysical Properties report
The Biophysical Properties report is an optional type of Report view that can be generated on demand. To open the Biophysical Properties report, do either of the following: Use the Report > Biophysical Properties from Document/Selection command. Use the View…
Text view
Protean 3D Interface » Views » Text 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…
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…
Hydropathy – Hopp-Woods
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Hydropathy – Hopp-Woods
The Hydropathy – Hopp-Woods track predicts protein antigenic determinants by searching protein sequences for the area of greatest local hydrophilicity. Hopp and Woods, 1981, make two assumptions in using hydrophilicity to find antigenic determinants: 1) antigenic…
Protean 3D toolbar
Protean 3D Interface » Protean 3D toolbar
The toolbar is located below the Protean 3D menus, and can be shown or hidden using the Controls > Show/Hide Toolbar command. The first two tools on the left of the toolbar affect the entire Protean 3D project, while the remaining tools affect only the Structure view. …
Domains & Sites (PROSITE)
Protean 3D Interface » Panels » Tracks panel » Track Options section » Database tracks » Domains & Sites (PROSITE)
The Databases – Domains & sites (PROSITE) track searches chains against common patterns found in the PROSITE database (installed with your software). When you apply the method, Protean 3D will search the protein sequence against the pattern library and display…
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.…
Secondary Structure – Deleage-Roux
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Secondary Structure – Deleage-Roux
The Secondary Structure – Deléage-Roux track predicts secondary structure using the approach of Deléage and Roux, 1987. The method uses an independent prediction of the protein’s structural class to bias the prediction of its secondary structure.…
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…
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…
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…
Report view
Protean 3D Interface » Views » Report view
Protean 3D offers a variety of different Report views, depending on the structure or result (variant search, BLAST search) being viewed. If the entire sequence or “nothing” is selected, the report applies to the entire protein. If an entire multi-chain…
Secondary Structure – Garnier-Robson
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Secondary Structure – Garnier-Robson
The Secondary Structure – Garnier-Robson track , from Garnier et al. (1978), Garnier and Robson (1990), and Garnier, Gibrat and Robson (1996), predicts protein structure from the amino acid sequence. The method examines the propensity of a given residue to…
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…
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. …
Use basic editing commands
Miscellaneous Tasks » Use basic editing commands
Protean 3D’s basic editing commands are similar to those found in Microsoft Windows and other text editing programs. Task Command Keyboard shortcut Notes To remove a portion of text Edit > Cut Ctrl/Cmd+X Text is placed…
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…
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…
NovaDock AI wizard: Sequences
Predict Structures, Antibody Interactions and Docking » Run Nova applications within the Protean 3D interface » Run NovaDock AI through Protean 3D » NovaDock AI wizard: Sequences
When you predict docking interactions with NovaDockAI, the wizard begins with the Sequences screen. This screen is used to specify the protein sequences to use for the prediction(s). The number of sequences you can enter/upload to submit for folding depends on your…
Pairwise view
Protean 3D Interface » Views » Pairwise 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…
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…
NovaFold-related tracks
Protean 3D Interface » Panels » Tracks panel » Track Options section » NovaFold-related tracks
After running a NovaFold prediction and opening the result file (.novafold), the Tracks panel displays tracks specific to this type of prediction. To apply this track to the sequence: Tracks related to NovaFold predictions are listed below. In the Tracks panel,…
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…
NovaDock Report: Model
Protean 3D Interface » Views » Report view » NovaDock report » NovaDock Report: Model
Below the Model Overview section of the NovaDock Report are expandable sections for each of the individual models (e.g., Model 1, Model 2, etc.). To view or hide this section of the report, click on the expand arrow (small blue triangle) in its header. The image in…
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…
Cleavage Sites (Proteases)
Protean 3D Interface » Panels » Tracks panel » Track Options section » Database tracks » Cleavage Sites (Proteases)
The Cleavage sites (Proteases) track predicts cleavage sites for proteases (also termed peptidases or proteinases) and chemicals in a protein sequence using known proteolytic signatures. When you apply Cleavage sites (Proteases) to the Analysis view, Protean 3D…
Predictions view
Protean 3D Interface » Views » Predictions view
After launching NovaCloud Services, two views become available. The first of these is NovaCloud Services, which is used to log in and launch a setup wizard for NovaFold, NovaFold Antibody, or NovaDock predictions. Once a prediction has been started, you can monitor its…
(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…
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…
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 >…
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…