BV_FindingBindingPockets

Finding and Visualizing a Binding Pocket

Via BALLViews python interface various tasks concerning binding pockets can be easily addressed. In our python tutorial section we offer help how to use our python interface.

In the following we discuss some general tasks:

• locating a binding pocket

In BALLView each molecular unit of a opened molecular file is shown in the hierarchic view of the Structures widget. First order is systen, than molecule, chains, residues and atoms. Selection of entities leads to a highlighting in the molecular scene. BALLView also offers a method to focus onto certain parts via the right mouse button context menu.

BALLView offers automatization for screening the Structures hierarchy via menu

User -> highlightLigand()

Furthermore, simple python scripts to select atoms or residues within a distance of a pre selected atom or residue can be found in BALL/source/EXAMPLES/PYTHON/BALLView/ namely selectNeighbourAtoms() or selectNeighbourResidues().

If data is taken from the PDB, the ligand information is often incomplete. You can either use the edit-mode to set the bond orders right, than try use the Saturate with hydrogen tool (Build - Saturate with hydrogens) to fill up free valences with hydrogens. If on the other hand you specify the hydrogens manually via the edit mode, you can use BALL's bond order assigner to compute all co- or even sub-optimal bond order assignments for the ligand.

• creating a visualization

BALLView offers a predefined script to create a Ball-and-Stick model of the ligand, while the remainder of the molecule is shown as Cartoon model.

User -> showCartoonAndLigand()

BALLView in general offers multiple representations. The user can easily create individual binding site views. A typical example would be ball-and-stick for ligand, semi transparent ligand VdW surface, SES surface of binding pocket, and secondary structures of all chains. The corresponding atoms/residues for which a representation has to be created can be specified by highlighting the entities (atoms, chains, ..) in the Structures widget. The once created representations can be switched on and off in the Representations widget.

Also BALLView's project file format (*.bvp) allows storing all created representations.

Export of the molecular scene to png is easily possible. If you have a raytracing supported version...

Given a binding pocket, e.g. by residue id's, the user can use BALLViews selection mechanism to select user specified molecular entities. Further information on how to use BALLViews expression bar can be found in our BALLView expression tutorial.

• compare and map binding sites and ligands

The BALL library offers a StructureMapper....