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(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…
(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…
Track Options section
Protean 3D Interface » Panels » Tracks panel » Track Options section
The Track Options section is located in the Tracks panel and provides an editable display of options for a selected Protean 3D track. Opening the Track Options section: Do either of the following: Click the expand bar entitled “Options” Use View > Tracks >…
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…
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…
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 >…
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…
Lighting section
Protean 3D Interface » Panels » Style panel » Lighting section
The Lighting section, located in the Style panel, allows you to change lighting characteristics of the Structure view. Up to three “directional” lights may be deployed, in addition to displaying “ambient” light. The following video shows the…
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…
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…
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…
NovaFold wizard: Options
NovaFold: protein structure prediction » 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…
NovaDock wizard: Options
NovaDock: protein-protein docking » 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…
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…
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…
NovaFold Antibody wizard: Options
NovaFold Antibody: antibody interaction prediction » 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…
Part C: Edit track options
Protean 3D Interface » Views » Analysis view » Try it! – Apply tracks to the Analysis view » Part C: Edit track options
This tutorial follows Part B: Compare results from two tracks. Scroll down the Analysis view to the Flexibility-Karplus-Schulz track. Click on the plus sign to reveal two sub-plots called Flexibility Regions and Flexibility Plot. Note that under the current…
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. …
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.…
Panels
Protean 3D Interface » Panels
Settings panels allow you to optimize the look, contents and layout of the Protean 3D view. To learn what can be done within each panel and their expandable sections, click the links below. Panel name Sections within the panel Explorer …
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,…
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…
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 Antibody wizard: Submit
NovaFold Antibody: antibody interaction prediction » Run NovaFold Antibody through Protean 3D » NovaFold Antibody wizard: Submit
When you predict antibody interactions with NovaFold Antibody, the third wizard screen is Submit. This screen displays the prediction jobs that were set up in the Sequences and Options screens, but have not yet been run. Click Submit to accept the terms of the…
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…
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…
Run NovaFold Antibody through Protean 3D
NovaFold Antibody: antibody interaction prediction » Run NovaFold Antibody through Protean 3D
This topic is a general overview on how to set up, run and view a NovaFold Antibody prediction through the Protean 3D interface. If you are instead running NovaFold Antibody locally on a Linux or Macintosh machine, see Run Nova applications locally. If you are running…
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…
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…
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 on one of the atoms within the desired…
Predicted Protein Function
Protean 3D Interface » Views » Report view » NovaFold report » NovaFold Report: Model » Predicted Protein Function
If you checked Predict ligand binding sites and protein function in the NovaFold Options screen, the Predicted Protein Function section of the NovaFold Report is available for Model 1, and for any model with a predicted TM-score ≥ 0.5. This section shows…
Tracks panel
Protean 3D Interface » Panels » Tracks panel
The Tracks panel, represented by a graph icon (), provides a list of prediction tracks sorted by classification. Prediction tracks are used to evaluate the sequence and structural characteristics of a protein. Results of tracks chosen in this panel are displayed in the…
Examples of surface types
Protean 3D Interface » Panels » Explorer panel » Surfaces section » Examples of surface types
Two types of surfaces and three levels of surface resolution are available, and are controlled via options in the Surfaces and Rendering sections. The following images show the identical portion of a structure using the six different rendering choices. All images are…
Hydropathy – Parker
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Hydropathy – Parker
The Parker track uses the method of Parker et al., 1986, which is a hydrophilicity scale based on high-performance liquid chromatography retention times of model synthetic peptides. Hydrophilicity measures have been used extensively in the prediction of antigenic amino…
Amphiphilicity (Eisenberg)
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Amphiphilicity (Eisenberg)
The Amphiphilicity (Eisenberg) track predicts the Eisenberg Moment using the approach of Eisenberg et al., 1984. Hydrophobic moments are semi-empirical quantities based on computation and experimental measurements, which describe the distribution of hydrophilic and…
Surface Probability (Emini)
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Surface Probability (Emini)
The Surface Probability (Emini) track predicts the probability that a given region lies on the surface of a protein, using the approach of Emini et al., 1985. To apply this track to the sequence: In the Tracks panel, check the box next to Surface Probability…
Antigenicity – Welling
Protean 3D Interface » Panels » Tracks panel » Track Options section » Immunogenicity tracks » Antigenicity – Welling
The Welling track predicts antigenicity using the method of Welling et al., 1985. Previous methods assumed that antigenic regions were mainly hydrophilic regions on the surface of a protein. By contrast, the Welling method is based on the percentage of each amino acid…
Flexibility (Karplus-Schulz)
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Flexibility (Karplus-Schulz)
The Flexibility (Karplus-Schulz) track predicts backbone chain flexibility using the approach of Karplus and Schulz, 1985. The method is useful for resolving antigenic sites, as these regions tend to be among the most flexible in a polypeptide sequence. To apply…
Stability – Aliphatic Index
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Stability – Aliphatic Index
The Stability – Aliphatic Index track (Gasteiger et al. 2005) predicts regional stability by calculating the relative volume occupied by aliphatic side chains. This is a positive indicator of globular protein thermostability. This method is only available for…
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…
Similar Experimental Structures
Protean 3D Interface » Views » Report view » NovaFold report » NovaFold Report: Model » Similar Experimental Structures
The Similar Experimental Structures section of the NovaFold Report is visible only if you checked Predict ligand binding sites and protein function in the NovaFold Options screen. Rank - Displays a list of the ten most similar templates, with “1”…
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…
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…
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…
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…
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…
Transmembrane – Goldman-Engleman-Steitz
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Transmembrane – Goldman-Engleman-Steitz
The Transmembrane – Goldman-Engleman-Steitz track predicts non-polar alpha helices which may span a cell membrane, using the approach of Engleman et al., 1986. To search for non-polar helices, scales of residue polarity are applied across a protein sequence. This…
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…
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…
Stability – Instability Index
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Stability – Instability Index
The Stability – Instability Index track estimates the stability of the protein in a test tube. The Instability Index is calculated using the approach of Guruprasad et al., 1990,, which predicts regional instability by calculating the weighted sum of dipeptides…
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…
Secondary Structure – Chou-Fasman
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Secondary Structure – Chou-Fasman
The Secondary Structure – Chou-Fasman track predicts secondary structure of proteins from the crystallographic structures of their amino acid sequences. Secondary structure prediction methods from the1970s and 1980s rely on the propensities of individual…
T-Cell Epitopes – Rothbard-Taylor
Protean 3D Interface » Panels » Tracks panel » Track Options section » Immunogenicity tracks » T-Cell Epitopes – Rothbard-Taylor
The T-Cell Epitopes – Rothbard-Taylor track locates potential T-lymphocyte antigenic determinants which contain a common sequence motif. Although Rothbard and Taylor, 1988, found that the method predicted 80% of the antigenic determinants for their peptide…
Create or Find Variants using Protein Design
Create or Find Variants using Protein Design
Protein Design, accessed through Protean 3D, lets you make one or more changes at the residue-level on a protein structure, and calculates whether these changes are likely to be stabilizing or destabilizing compared to the original structure. Two workflows are…
Charge Density (Lehninger)
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Charge Density (Lehninger)
The Charge Density (Lehninger) track predicts regions of positive and negative charge by summing charge over a specific range of residues. DNASTAR developed this method using the pK tables of Lehninger, 2005. Since charged residues tend to lie on the surfaces of…
Transmembrane – TopPred
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Transmembrane – TopPred
The Transmembrane – TopPred track utilizes hydropathy analysis to propose probable transmembrane regions in a protein sequence, using the methods of von Heijne, 1992, and Claros and von Heijne, 1994. Possible membrane-protein topologies are considered and…
Modifications (SUMOylation) track
Protean 3D Interface » Panels » Tracks panel » Track Options section » Modifications (SUMOylation) track
The Modifications (SUMOylation) track predicts sites where lysine undergoes the addition of small, ubiquitin-like modifiers after translation using the approach of Ren et al., 2009. The covalent attachment of this small, ubiquitin-like protein to other proteins…
Details panel
Protean 3D Interface » Panels » Details panel
The Details panel, represented by a blue “information” icon (), lets you view details about the structure, sequence or selection. Information in this section is updated continuously to reflect the currently selected data. Opening the Details panel: Do any of the…
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.…
NovaFold Report: Templates
Protean 3D Interface » Views » Report view » NovaFold report » NovaFold Report: Templates
In NovaFold, protein fragments from existing PDB structures are used as templates for building a prediction model. The Templates section of the NovaFold Report lets you compare the sequence similarity of a query sequence to the top ten template sequences in MegAlign…
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…
NovaDock wizard: Structures
NovaDock: protein-protein docking » 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…
T-Cell Epitopes – AMPHI
Protean 3D Interface » Panels » Tracks panel » Track Options section » Immunogenicity tracks » T-Cell Epitopes – AMPHI
The T-Cell Epitopes – AMPHI track uses the model of Margalit and Berzofsky, 1987 to predict immunodominant helper T-lymphocyte antigenic sites from primary sequence data. The underlying assumption of the AMPHI method is that T-cell antigenic sites are composed of…
Antigenicity – Jameson-Wolf
Protean 3D Interface » Panels » Tracks panel » Track Options section » Immunogenicity tracks » Antigenicity – Jameson-Wolf
The Jameson-Wolf track predicts potential antigenic determinants by combining existing methods for protein structural predictions, using the approach of Jameson and Wolf , 1988. Method results appear as multiple peaks in the Antigenic Index plot, with each peak…
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…
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…
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…
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…
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,…
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…
Examples of rendering styles
Protean 3D Interface » Panels » Style panel » Rendering section » Examples of rendering styles
In the Rendering section, the following choices are available in all of the first three drop-down menus: Sticks Spheres Ball and Stick Points Wireframe Invisible These choices…
NovaFold wizard: Submit
NovaFold: protein structure prediction » Run NovaFold through Protean 3D » NovaFold wizard: Submit
When setting up a NovaFold prediction in Protean 3D’s NovaFold wizard, the third screen is Submit. This screen displays the prediction jobs that were set up in the Sequences and Options screens, but have not yet been run. Click Submit to accept the terms of…
NovaDock wizard: Submit
NovaDock: protein-protein docking » Run NovaDock through Protean 3D » NovaDock wizard: Submit
The Submit screen is the third of three screens in the NovaDock prediction wizard and displays the prediction jobs that were set up in the Structures and Options screens, but have not yet been run. Click Submit to accept the terms of the license agreement and…
Database tracks
Protean 3D Interface » Panels » Tracks panel » Track Options section » Database tracks
The Tracks panel lets you choose which database tracks to apply to the Analysis view. The following links describe the methods and explain how to change their Track Options settings, if you desire to do so: Cleavage sites Domains & sites
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…
Filter text search results
Search for Sequences Online » Search for text or accession number matches (Entrez) » Filter text search results
When you press the Filter results tool () in the header above the Table or Pairwise views, there are two options: Filter and Clear Filter. Clicking on the Filter option opens the following dialog: Use the drop-down menu to choose a filter type, then enter the…
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…
Search for Sequences Online
Search for Sequences Online
This application lets you search National Center for Biotechnology Information (NCBI) databases for matches to text or sequence that you specify. Query part or all of a nucleotide or protein sequence against one of NCBI’s sequence databases using the Basic…
Disorder (JRONN)
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks » Disorder (JRONN)
The Disorder (JRONN) track predicts disordered regions of proteins, which are unlikely to form well-defined three-dimensional structures. These regions may affect both solubility and the ability to crystallize. DNASTAR developed this track based on the regional order…
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…
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…
A Protein Design result
Protean 3D Interface » Panels » Details panel » A Protein Design result
If a Protein Design result is open, the Details panel contains the following information: Title The name of the Protein Design job. Summary Structure – The name of the parent structure. Chain and Position …
Filter hot spot scan results
Protean 3D Interface » Views » Report view » Protein Design reports (Variants and Hot Spot Scan) » Filter hot spot scan results
When you press the Filter results tool () in the header above the Hot Spot Scan report, there are two options: Filter and Clear Filter. Clicking on the Filter option opens the following dialog: Use the drop-down menu to choose a filter type, then enter the…
Immunogenicity tracks
Protean 3D Interface » Panels » Tracks panel » Track Options section » Immunogenicity tracks
The Tracks panel lets you choose which immunogenicity tracks to apply to the Analysis view. The following links describe the methods and explain how to change their Track Options settings, if you desire to do so: Antigencity: Jameson-Wolf Welling B-cell…
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.…
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…
NovaFold Report: Molecule
Protean 3D Interface » Views » Report view » NovaFold report » NovaFold Report: Molecule
The Molecule section of the NovaFold Report contains the number of residues in the sequence and the query sequence that was submitted for folding. The next section of the NovaFold Report is the Templates section.
Filter sequence search results
Search for Sequences Online » Search for text or accession number matches (Entrez) » Filter sequence search results
When you press the Filter results tool () in the header above the Table or Pairwise views, there are two options: Filter and Clear Filter. Clicking on the Filter option opens the following dialog: Use the drop-down menu to choose a filter type, then enter the…
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. …
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…
Explorer panel
Protean 3D Interface » Panels » Explorer panel
The Explorer panel, represented by a compass icon (), includes two expandable sections that allow you to view, select or hide structural elements and to apply surfaces to the structure. Opening the Explorer panel: Do any of the following: Click on the Explorer…
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.…
Search wizard: Search
Search for Sequences Online » Search for sequence matches (BLAST) » Search wizard: Search
The Search screen is the second of four screens in the BLAST Search wizard. The Search screen is used to choose the BLAST program and database. Specify whether you wish to search for Nucleotides or Proteins. Select the desired BLAST program from the Using…
Run NovaFold through Protean 3D
NovaFold: protein structure prediction » Run NovaFold through Protean 3D
This topic is a general overview on how to set up, run and view a NovaFold prediction through the Protean 3D interface. If you are instead running NovaFold locally on a Linux or Macintosh machine, see Run Nova applications locally. If you are running NovaFold online,…
Run NovaDock through Protean 3D
NovaDock: protein-protein docking » Run NovaDock through Protean 3D
This topic is a general overview on how to set up, run and view a NovaDock prediction through the Protean 3D interface. If you are instead running NovaDock locally on a Linux or Macintosh machine, see Run Nova applications locally. If you are running NovaDock online,…
Biophysics tracks
Protean 3D Interface » Panels » Tracks panel » Track Options section » Biophysics tracks
The Tracks panel lets you choose which biophysics tracks to apply to the Analysis view. The following links describe the methods and explain how to change their Track Options settings, if you desire to do so: Amphiphilicity Charge Density Disorder…
Search for sequence matches (BLAST)
Search for Sequences Online » Search for sequence matches (BLAST)
The BLAST Search wizard is used to search a query sequence against one of NCBI’s databases. The sequence can be part or all of an active sequence, another sequence file on your computer, or typed/pasted-in text. The wizard consists of four consecutive screens,…
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…
View progress and see variant results
Create or Find Variants using Protein Design » View progress and see variant results
Once you have pressed the Run button in the Protein Design wizard, you can use the Jobs panel to monitor progress, stop the run, or open results. After the variant has been created, the following views and panels can be used for analysis: The Protein Design…
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…