Term Project — Final Report (80% of the term project)¶

Deadline¶

Warning

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

The final report is the complete, final version of your term project deliverables:

Important

This is the continuation of your Mid-Report, not a separate/independent report.

Everything you did in the Mid-Report must be included here again (as needed), reproduced and improved.
If you received feedback/corrections (rubric, instructor notes, TA comments), you must apply those corrections in the final report.

Submit two items:

Note

Your archive should follow the same clean, reproducible folder/file practices introduced in the pre-labs.

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.

Your final report must be a properly formatted scientific report and should include (at minimum):

Cover page
Table of contents
Introduction
Methodology (with tools, databases, and parameters/settings when relevant)
Results and Interpretation (figures/tables + interpretation + conclusions)
Discussion / Limitations (what is reliable vs uncertain, limitations of tools and data)
Conclusion
References
Appendices (optional)

Note

The quality of interpretation is essential. Outputs without explanation will not receive full credit.

In addition to including and improving Mid-Report work, your final project must include the following.

Your homology modeling section must include:

Pairwise alignment

Show and interpret at least one relevant pairwise alignment (e.g., target vs template). Discuss identity/similarity, gaps, and implications for model quality.
Multiple sequence alignment (MSA)

Include an MSA of the target with selected homologs/templates (as appropriate) and interpret conserved regions/motifs.
Comparison of models used

If you generated more than one model or used multiple templates/settings, compare them clearly.

Your comparison should explain what changed between models (template choice, alignment, parameters) and justify which model(s) you selected for downstream steps.

Your project files should be organized so that a reviewer can understand what you did without guessing.

Include (as applicable):

Sequences used (FASTA)
Alignments (raw output files if available)
Models/structures you generated (e.g., PDB/mmCIF as applicable)
Docking-related outputs: poses, docking logs/summaries, ligand files, etc.
High-quality figures (original/high-resolution versions, not only embedded in the PDF)
A short README file describing:
- What each file/folder contains
- Which tool generated it
- The minimal steps to reproduce key results (brief but clear)

Tip

Use a clear folder structure (for example: data/, results/, figures/, models/, docking/, scripts/) consistent with the pre-labs.

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
File package is organized and includes a README