BV_ToolsForProteins

Functionality for working with proteins in BALLView

Most of the functionality that is implemented in BALL is also provided in BALLView.

BALLView consist of a number of widgets, e.g. the Structures , Representations, scene widget and many more.

TODO: image

In the following we give a non-exhaustive overview of functionality aiming specifically at proteins. For general functionality like visualization/representation modes, the BALL-project file type, stereoscopic visualization, XML3D export, shortcuts or the Edit mode please have a look at the BALLView Tutorial page wiki/Tutorials.

• Download from PDB

  Directly download protein structures by their PDB identifiers into BALLView. Depending on the current default representation, the protein directly appears in the scene widget.

• PeptideBuilder

  Create a peptide by entering the amino acid sequence in BALLView

• Add Peptide Endcaps

• Check Structure

• Build bonds

• Add missing atoms, e.g. hydrogens

  Note: the hydrogen positions are not set automatically. Sensible positions can be found using an energy minimization (Link TODO - the School/Teacher tutorial has it)

• Secondary Structure Processor

  BALLView offers a DSSP implementation via Tools -> Calculate Secondary Structure

• Hydrogen Bond Processor

  Based on the DSSP algorithm, hydrogen bonds can be computed and visualized (Tools -> Calculate H-Bonds)

• Rotamer Assignment

  Based on the Dunbrake Rotamer Library, each residues rotamer state can be manipulated. Context menu of the Structures widget.

• Selection by BALL Expressions or SMARTS

  The Structures is supplemented with an integrated search tool, where the user can specify so-called BALL expressions to select molecular entities. A full documentation can be found here (TODO). A tutorial can be found here (wiki/BV_ExpressionBar).

• Disulfid bonds

  Connect and disconnect residues by disulfid bonds via the context menu of the Structures widget.

• ForceFields

  AMBER, CHARM, MMFF94

• Electron desity maps from EDS or EMDB

• Binding pockets See : [wiki/BV_FindingBindingPockets]