Protein Interaction Hypothesis Using AlphaFold3 & ChimeraX - 12/06/2025 12:52 EDT
Budget: $250 – $750 USD
Design a testable protein-protein or protein-nucleic acid interaction hypothesis using AlphaFold3 (AF) and ChimeraX from one of the provided protein options (.xlsx file attached).
This is an undergraduate course project, not a research-level or business project. The stakes are low and does not need to be perfect.
AF requirements: A minimum of 1 protein-protein or protein-nucleic acid predicted interaction (max 3). You must determine if each interaction is: electrostatic, hydrophobic, has key hydrogen bonding, etc. You must assign some degree of confidence outside of AF that this interaction may be relevant (Sequencing conservation? Post-translational modifications? Disease causing variants? Known mutational analysis?). You must ‘check’ your identified interaction in a minimum of 1 other AF predicted model (max 3).
.cxc requirements: With your provided files I should be able to open and run your .cxc file with no major problems. Your .cxc file should only display one of the protein-protein or protein-nucleic acid interacting regions that you want to display. Everything else that is not important should be ‘hidden’. If you want to set your camera to the view and molecule settings that you have submitted as a figure for this assignment, that is OK!
Figures: You must upload figures of your AF ChimeraX validation (determining how the proteins interact with each other). Your figures will likely depict different model views but please make sure that they have the same camera setting OR when you need to look at the ‘back’, that you clearly state this in your ‘figures’ file. Uploading your figures as a Google Slides document will be best mechanism here. You can use the ‘presenter notes’ to add if appropriate comments and details as necessary.
Reading assignment portion: Use Pubmed to find a recent Review article (2015 the latest timeframe) on your protein of
interest. Everyone’s review article will likely vary by length. Make sure you at least read the
introduction of your review article and then a few of the pertinent topic headers that are of interest to you and any ‘future directions’ for the field/protein/problem you are interested in. Write at least a 1 page over of your protein of interest. Please make sure you address the following points in your writing:
1.) What is the general biology of your protein of interest (if you want to state this in the
context of its interacting partner, even better!).
2.) Why should we care about understanding this protein and its structure/function?
3.) Why are you interested in this protein?
Specific rubric for this reading portion:
Structure, writing mechanics, and organization – 5 pts
(i) Writing is well organized and paragraphed.
(ii) Meets 250 minimum word target (one page, double-spaced).
(iii) Author paraphrases and does not directly quote from source when needed.
(iv) Use citations appropriately.
(v) Well-edited and revised for readability.
(vi) Minimal spelling or grammatical errors.
Demonstrated understanding – 5 pts
(i) Demonstrates understanding of the protein’s basic biology.
(ii) Can argue why studying this protein is important.
Content clarity – 5 pts
(i) The author clearly articulates their points.
(ii) The writing is purposeful and does not contain ‘fluff’.
(iii) The writing progresses with a logical flow.
File naming requirements:
AF3 settings: Lastname_AF3
.cif files: model_a.cif (this will be for the model you have the most confidence in) model_b.cif (this will be for the alternative model)
.json files: model_a.json (this will be for the model you have the most confidence in)
model_b.json (this will be for the alternative model)
Multiple sequence alignments: .aln or .clustal files are acceptable. protein_a.aln (or protein_a.clustal) protein_b.clustal (or protein_b.aln).
Reading assignment: Reading Assignment is fine.
Figures: Figures is fine.
This is an undergraduate course project, not a research-level or business project. The stakes are low and does not need to be perfect.
AF requirements: A minimum of 1 protein-protein or protein-nucleic acid predicted interaction (max 3). You must determine if each interaction is: electrostatic, hydrophobic, has key hydrogen bonding, etc. You must assign some degree of confidence outside of AF that this interaction may be relevant (Sequencing conservation? Post-translational modifications? Disease causing variants? Known mutational analysis?). You must ‘check’ your identified interaction in a minimum of 1 other AF predicted model (max 3).
.cxc requirements: With your provided files I should be able to open and run your .cxc file with no major problems. Your .cxc file should only display one of the protein-protein or protein-nucleic acid interacting regions that you want to display. Everything else that is not important should be ‘hidden’. If you want to set your camera to the view and molecule settings that you have submitted as a figure for this assignment, that is OK!
Figures: You must upload figures of your AF ChimeraX validation (determining how the proteins interact with each other). Your figures will likely depict different model views but please make sure that they have the same camera setting OR when you need to look at the ‘back’, that you clearly state this in your ‘figures’ file. Uploading your figures as a Google Slides document will be best mechanism here. You can use the ‘presenter notes’ to add if appropriate comments and details as necessary.
Reading assignment portion: Use Pubmed to find a recent Review article (2015 the latest timeframe) on your protein of
interest. Everyone’s review article will likely vary by length. Make sure you at least read the
introduction of your review article and then a few of the pertinent topic headers that are of interest to you and any ‘future directions’ for the field/protein/problem you are interested in. Write at least a 1 page over of your protein of interest. Please make sure you address the following points in your writing:
1.) What is the general biology of your protein of interest (if you want to state this in the
context of its interacting partner, even better!).
2.) Why should we care about understanding this protein and its structure/function?
3.) Why are you interested in this protein?
Specific rubric for this reading portion:
Structure, writing mechanics, and organization – 5 pts
(i) Writing is well organized and paragraphed.
(ii) Meets 250 minimum word target (one page, double-spaced).
(iii) Author paraphrases and does not directly quote from source when needed.
(iv) Use citations appropriately.
(v) Well-edited and revised for readability.
(vi) Minimal spelling or grammatical errors.
Demonstrated understanding – 5 pts
(i) Demonstrates understanding of the protein’s basic biology.
(ii) Can argue why studying this protein is important.
Content clarity – 5 pts
(i) The author clearly articulates their points.
(ii) The writing is purposeful and does not contain ‘fluff’.
(iii) The writing progresses with a logical flow.
File naming requirements:
AF3 settings: Lastname_AF3
.cif files: model_a.cif (this will be for the model you have the most confidence in) model_b.cif (this will be for the alternative model)
.json files: model_a.json (this will be for the model you have the most confidence in)
model_b.json (this will be for the alternative model)
Multiple sequence alignments: .aln or .clustal files are acceptable. protein_a.aln (or protein_a.clustal) protein_b.clustal (or protein_b.aln).
Reading assignment: Reading Assignment is fine.
Figures: Figures is fine.