What file types are supported for protein structure analysis?
Protean 3D supports protein structure files from the Protein Data Bank (*.pdb, *.ent, *.pdb.gz, *.ent.gz, *.zip, *.txt), as well as structure files created by Protean 3D (*.structure) or one of our Nova Applications (*.novafold, *.antibody, *.novadock).
Can I customize the appearance of my protein structure?
Yes. Protean 3D offers unmatched flexibility in customizing the appearance of your protein structure. First select the molecule(s) you wish to edit, then access the Styles panel where you can adjust the rendering, color, and lighting for your protein structure.
How can I annotate my protein structure?
To create an annotation on your protein structure, first select the structural element you wish to annotate and then choose Features>New Feature. The Options area of the Features panel automatically becomes populated with a default name, as well as information about the molecule and endpoints of the feature.
How do I apply protein sequence analysis methods to analyze biophysical properties and predict secondary structures?
To analyze biophysical properties and predict secondary structures on your protein sequence, select the desired method from the Tracks panel, located by default on the right side of the Protean 3D window. The Analysis view displays a graphical representation of all of the tracks that have been applied to the active sequence or structure.
How can I identify similarities between multiple protein structures?
You can use Protean 3D to easily perform protein structural alignments of entire macromolecular structures or selected regions. Simply add your structure files or open your NovaFold results, then select the chains you wish to align and choose Structure>Align Structures. Following your protein structural alignment, evaluate RMSD values for aligned structures to determine their divergence from one another.
What types of surfaces can I create on my protein structure?
Protean 3D allows you to easily create molecular and solvent accessible surfaces around your structure to clearly view structural elements of interest relative to the protein surface. To apply a molecular surface or a solvent accessible surface, click on the Create a surface button, located in the Surfaces area of the Explorer panel. Choose the surface style and speed from the drop down list provided to create a surface for the current selection, or for all chains, if nothing is selected.
How can I see the impact of a mutation on my protein structure?
Protean 3D includes protein stability prediction tools which allow you to make changes at the residue-level on a protein structure and predict whether these changes are likely to be stabilizing or destabilizing compared to the original structure. To introduce a variant, first select the residues you wish to mutate from the Sequence view . Then, choose Modeling > Protein Design > Create Variant With > Selection. Use the Substitute drop-down menus to select a different amino acid for each position of interest and then click Run. In most cases, protein mutation stability predictions are available in a matter of seconds.
What options are available for exporting my protein structure?
Protean 3D allows you to export the protein structure itself or an image of the structure for publication. To export your protein structure as a .pdb or .cif file, use Export Data > Export Structure. To export an image of your protein structure in .png, .jpg or .gif format, use File > Export Image > Structure.