Complete PS -

Proteome-wide in silico prioritisation of E. coli protein targets followed by 3D structure-based active-site analysis and molecular docking with key antibiotics.

This 4-week project uses a focused bioinformatics pipeline to identify and analyse promising E. coli protein targets for antibiotics. You’ll shortlist 2–3 essential, non-human-homologous proteins, obtain/model their 3D structures, predict active sites, and perform docking with selected antibiotics. The outcome is a concise but complete workflow linking rational target selection to drug–protein interaction analysis.

PS-Timeline

Week 1 – Setup, literature, proteome & initial filtering

Finalise organism (E. coli strain), antibiotics, and goal of the project (e.g. “identify potential antibiotic targets and study docking interactions”).

Quick literature review: 2–3 papers on proteome-wide target discovery + docking.

Retrieve E. coli proteome (UniProt) and make a simple spreadsheet (ID, function).

Mark obvious essential / classic targets from literature (e.g. GyrB, DHFR, PBPs) and pre-select ~10 candidates.

Week 2 – Shortlisting targets & structure preparation

Do non-homology check to human proteins for the ~10 candidates (BLASTp or literature-based justification).

Narrow down to 2–3 final targets based on essentiality + non-homology + druggability (justify in 1 table).

Retrieve or model 3D structures (PDB / SWISS-MODEL / AlphaFold).

Clean structures, check basic quality, and save final PDBs.

Week 3 – Active sites, ligand prep & docking