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Term Project — Mid-Report (20% of the term project)

Deadline

  • 03 May 2026

Warning

No late submission is allowed. Plan ahead for technical problems (PDF export, file upload, Turnitin processing, internet issues, etc.).

Purpose

The purpose of the mid-report is to help you receive feedback on:

  • Your protein choice and scientific justification
  • Your design for the term project
  • Your preliminary analysis results and your interpretation
  • Your plan for the remaining work until the final report

What to submit

  • Submit one PDF file only.

Ground rules

  • AI usage is encouraged, but the written report must respect the Turnitin AI detection limit.
  • Based on Turnitin AI detection, AI-similarity must be ≤ 25%.
  • Low similarity is expected for the report, but there is no fixed similarity percentage requirement. Overall quality will be evaluated.
  • Reports must be well formatted (include what is necessary for a proper report, e.g., cover page, table of contents, list of figures/tables when applicable, appendices if needed).
  • Use a sans-serif font, 12 pt, justified, with 1.5 or double spacing.
  • Any reference style is allowed, as long as it is consistent.
  • Report format is part of grading (proper caption placement for figures/tables, alignment, consistent numbering, readable visuals, etc.).
  • For figures, avoid low-quality screenshots that reduce resolution.

Protein selection requirements

Select a protein that satisfies all of the following:

  • Its amino acid sequence (or at least the coding sequence) is known.
  • There is no experimental 3D structure information for the target protein (e.g., no solved structure by X-ray / NMR / cryo-EM for the exact target).

  • The protein has a ligand binding domain.

    Note: substrates are also ligands, especially in docking.

  • The protein has conserved domains or regions that can be modeled with homology modeling.

  • A BLAST search is recommended to identify homologs and evaluate suitability for homology modeling.

Report structure (minimum)

  • Cover page
  • Table of contents

  • Introduction

    Provide concise scientific background, cite relevant literature, and explain your protein choice and reasoning.

  • Methodology

    Describe all tools, databases, and sources you used. Reference them properly and make sure they are accessible.

  • Results and Interpretation

    Present the outputs clearly (figures/tables) and interpret them.

  • Plan to the Final Report

    Provide a clear roadmap of what you will do next, what outputs you expect, and what criteria you will use to evaluate your results.

  • References

  • Appendices (optional)

Required analyses

1) Secondary structure prediction

  • Apply all three methods covered in the course, and also include one additional method of your choosing.
  • Compare the results across methods and comment on agreement/disagreement.

2) Sequence alignment and homology evidence

  • Use BLAST to identify homologs and potential template regions.
  • Include at least one meaningful alignment analysis (pairwise and/or multiple alignment), and interpret conserved regions/motifs.

Submission checklist

  • PDF only (single file)
  • Deadlines met (no late submissions)
  • Turnitin AI similarity ≤ 25%
  • Formatting requirements satisfied (font, spacing, justified text, report structure)
  • Figures/tables are readable, numbered, and captioned properly
  • References are consistent and all claims that require citations are cited
  • All analyses include interpretation and clear conclusions