01/What is Protein Folding?
Proteins are molecular machines that perform nearly every function in your body. They're built from chains of amino acids, but a chain alone is useless—it must fold into a precise three-dimensional shape to work. This shape determines everything: whether an enzyme can catalyze a reaction, whether an antibody can recognize a virus, whether a signal can pass between neurons.
When proteins misfold, the consequences can be devastating. Misfolded proteins can aggregate into toxic clumps, lose their function entirely, or gain harmful new properties. Understanding how proteins fold—and how mutations cause them to misfold—is one of the most important challenges in modern biology.
For decades, determining a protein's structure required years of laboratory work. In 2020, DeepMind's AlphaFold changed everything. This AI system can predict protein structures from amino acid sequences alone, with accuracy rivaling experimental methods. What once took years now takes minutes.
02/The Diseases We Study
Clarity Protocol focuses on neurodegenerative diseases—conditions where protein misfolding destroys the brain over time.
Alzheimer's Disease
Amyloid-beta, Tau
The most common form of dementia. Amyloid plaques and tau tangles accumulate in the brain, killing neurons and erasing memories. Mutations in amyloid precursor protein and tau can cause early-onset forms of the disease.
Parkinson's Disease
Alpha-synuclein
A movement disorder caused by the death of dopamine-producing neurons. Alpha-synuclein protein aggregates into Lewy bodies, spreading through the brain and disrupting motor control.
Frontotemporal Dementia
Tau, TDP-43, FUS
A group of disorders affecting personality, behavior, and language. Often strikes people in their 50s and 60s. Many cases are caused by mutations in tau or other RNA-binding proteins.
ALS
SOD1, TDP-43, FUS
Amyotrophic lateral sclerosis progressively paralyzes the body by killing motor neurons. Several genes linked to ALS encode proteins prone to misfolding and aggregation.
03/Why This Matters
Neurodegenerative diseases represent one of the greatest healthcare challenges of our time.
By 2050, the number of people with dementia is projected to reach 139 million. Current treatments only manage symptoms—none can stop or reverse the underlying disease. We need to understand these proteins at the atomic level to develop therapies that actually work.
Every mutant protein structure we analyze is a potential clue. Understanding how a single amino acid change affects protein folding could reveal why some mutations cause aggressive early-onset disease while others are benign. This knowledge is essential for developing targeted treatments.
04/How Clarity Protocol Works
Clarity Protocol is an autonomous research pipeline. It continuously monitors scientific literature for newly discovered protein variants, predicts their three-dimensional structures, analyzes the structural consequences of mutations, and generates research summaries—all without human intervention.
The system combines structure prediction with computational analysis and AI-powered interpretation. When a variant is processed, the pipeline doesn't just produce a structure—it compares that structure against wild-type proteins, identifies destabilized regions, and connects findings to relevant published research.
Everything is made publicly available as it's generated. Structures can be explored interactively. Analysis results are presented alongside AI summaries that explain findings in accessible language while maintaining scientific accuracy.
05/A Letter From the Founder
I have been led down this path against my will, yet I am grateful for where it has gotten me, and where it is going.
I do not want to bore you with the details, but I will do my best to quickly summarize a little bit of my story. I recently started school again as a software engineering major after a few year hiatus of pursuing other things. It has been amazing to feel the gears turning again after leaving my brain on idle for so long, and I thank God everyday for elasticity. Truly an amazing feat. After watching "The Thinking Game" (a documentary that covers Demis Hassabis' journey with DeepMind (highly recommend btw)), I became fascinated with protein folding. I, like many others, had never even heard of the concept, let alone the advancements DeepMind has made in it in recent years. This hit close to home because I have watched members of my family battle cancer, become riddled with dementia, etc... and I realized how amazing it was that I could contribute to the search for solutions. I had a PC in my room collecting dust and decided it was time to put that dinosaur to work.
Now knowing what I could do with tools like AlphaFold, ColabFold, and Folding@Home, I was left with the question "why isn't this more popular?". Many people have access to these open source tools, computers are becoming increasingly more powerful, why aren't they being put to use in their downtime? My opinion is that it is somewhat gated by the medical and biomechanical jargon involved. Yes, people can run it at home, but I do not think they are as motivated to do so if they do not fully understand what they are doing. My goal is to popularize these tools by making them more efficient through automation, and easier to understand with generated summaries and published references. I am hoping that by giving people clarity on the impacts they can make with the tools in their possession, they will choose to also contribute to the cause.