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.
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.
Open fullsizeAbove: 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 While it has been superseded by more modern tools, Zeus remains a proud part of my portfolio as a showcase of my ability to utilise my skills computer science and chemistry to serve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
Supports various industry & academic standard file formats:
Remote Download a PDB from RSCB server
Powerful Sequence Searching capabilities:
Wildcard search capability
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.
Ball and Stick
Ball and Wire
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.)
as a bitmap
Atom and Bond ListsExport
as a bitmap
Atom and Bond ListsControl
of rendering quality
to allow user flexibility with performance/rendering quality