Search
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…
Save and Export
Save and Export
Click on one of the links below to learn how to: Save a document Export a still image Export a structure file Export a 3D model of the structure Export an animation or video Save or export a report
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…
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…
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…
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.…
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…
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…
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.…
Align Multiple Structures
Align Multiple Structures
Homologous proteins often have similar structures. A structure alignment attempts to identify these similarities by comparing the shape and 3D conformation between two structures. Unlike simple superposition methods, structure alignments do not require prior knowledge…
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 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: protein-protein docking
Predict Structures, Antibody Interactions and Docking » Types of predictions » NovaDock: protein-protein docking
NovaDock is one of two protein docking applications that run within the Protean 3D interface, with the other being NovaDock AI. DNASTAR provides NovaDock as a local or cloud-based, separately licensed service within Protean 3D. NovaDock’s algorithm is based on…
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…
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…
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…
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…
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…
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.…