Zeus Molecular Viewer and Visualisation software

October 2010

During the course of completing my master's degree in Pharmacy and Chemistry, I developed Zeus, a molecular visualisation tool that allowed me to label and view specific residues in Brookhaven PDB (Protein Databank) molecular structures.

While current technologies have evolved towards JavaScript-based molecular viewers, Zeus remains an enduring testament to technical innovation and practical application. Written in Delphi Pascal / OpenGL for Windows — with a later version, Zeus-Android, written specifically for mobile devices using Java / OpenGLES — Zeus seamlessly bridged the divide between complex computational modelling and user-friendly interface design.

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Above: Zeus rendering a fragment of dsDNA

Original Promotional Video from 2011:

The software was specifically designed to visualise the intricate details of protein structures, and it played a pivotal role in my M.Pharm research. I successfully leveraged Zeus to design putative PDZ binding ligands, with the goal of mitigating neurological excito-toxicity mediated by the PSD-95 Calcium channel.

Zeus's robust functionalities provided comprehensive molecular modelling, including a wide array of rendering modes, exhaustive atom and bond lists, and advanced sequence searching capabilities. It's core strengths were in residue labelling, creating compelling visual representations of molecular structures, features I frequently utilised during my research, and producing high-quality Ramachandran plots.

For instance, in my thesis, I used Zeus to generate a wireframe rendering of the PSD-95 protein, colour-coded by R-group nature. This allowed me to view the backbone residues (with the PDZ domain and J-1-a-asp ligand rendered as cylinders) clearly and intuitively. In another requirement, Zeus facilitated the accurate measurement of distances between key atoms, creating an insightful visual narrative for my docked PDZ binding ligand, Jamie-3-L-a-aspartyl, with PSD-95.
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Above: Zeus wireframe rendering of the PSD-95 protein, colour-coded by R-group nature, together with putative Jamie-1 ligand (green) bound to PDZ region (blue).

Today, Zeus stands as a testament to my technical prowess, innovative thinking, and ability to apply cutting-edge technologies to solve complex problems in molecular biology and drug design. While it has been superseded by more modern tools, Zeus remains a proud part of my portfolio as a showcase of my ability to utilise my skills computer science and chemistry to serve practical, scientific purposes.

Zeus provides the following features:
  • Rotate, Translate and Zoom into the molecular model
    • View by residue chain type
    • View by residues by Chain
  • Calculate Hydrogen bonds
  • View atoms and bonds within molecules
  • Residue labelling
  • Measure distances/angles

Supports various industry & academic standard file formats:

  • Brookhaven PDB
    • Remote Download a PDB from RSCB server
  • Mol format
  • Mol2/SYBYL format
  • XYZ format

Powerful Sequence Searching capabilities:

  • Sequence Search/Highlight
  • Wildcard search capability
  • Residue/Base keypad
  • Display molecular model residue sequence

Ramachandran plot of protein structure

  • Produce high quality Ramachandran plots of dihedral angles to easily elucidate secondary structure
  • Protein structure can be viewed through a list of calculated Psi, Phi and Omega dihedral angles for each of the amino acid residues in the sequence.
  • Plots can also be made on a user chosen/loaded bitmap image allowing a ramachandran graph to be plotted over a standard distribution.

Rendering Modes

  • Wireframe
  • Ball and Stick
  • Ball and Wire
  • Cylinders
  • Triangular Tubes
  • Square Tubes
  • Space-filling - uses Van der waal's Radii to size atoms appropriately

Peptide structure "Ribbon"

  • 3D Bezier Bernstein-based function through peptide/nucleic acid backbone
  • Supports ribbon, line or tube rendering

Flexible colour configuration

  • Select invididual Atom colours
  • Background colour/Gradient colours
  • Highlight residue/nucleic acid colour
  • Residue/Nucleic acid type colours
  • Colouring of residues (CPK, by type etc.)

Export rendering as a bitmap Exhaustive Atom and Bond Lists Export rendering as a bitmap Exhaustive Atom and Bond Lists Control of rendering quality to allow user flexibility with performance/rendering quality  

[ Download and Install (~5mb) - recommended ]

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