Not knowing your expertise, I’ll risk making a fool of myself.
But first, for everyone’s sake: ALPHAFOLD ISNT AN LLM
That isn’t what alphafold is. Under no circumstances is it anywhere near close to a “database of every way … proteins can fold.” At all. And to construe it as anything other than an attempt at a way to predict or simulate the potential three dimensional structure a protein can adopt will mislead people.
A protein does not have one shape. It has multiple. They’re dynamic. They change shape. It’s how proteins represent information. I’d argue that the ability of proteins to change their shape is one of their most important properties. (Analogy: play a song on an instrument with one note. Hard-mode: consider silence a note)
Everything in Alphafold is a GUESSED MODEL and not reality. Crystal structures and cryo-EM structures are also MODELS. But they’re based on empirical evidence.
Alphafold is based on statistical evidence. It is evidence, but it is weaker. If we don’t have an example of how a protein might fold in the structural database, alphafold will struggle to predict the structure. At least not without it sharing some type of sequence similarity.
I see this in the AI drug companies and how they just treat predictive models the same as 2 angstrom crystal structures and it pisses me off.
Not an expert at all, so thanks for clarifying what the alphafold project is in more detail. My bad on the confusing wording as well, i specifically mentioned my distrust of commodified llms to distinguish that from whatever alphafold and similar projects would be (don’t know if that use of ai has a specific term).
From what I know of the project it seems to be nice use of ai tech, am i wrong in that? Genuinely asking :)
Not knowing your expertise, I’ll risk making a fool of myself.
But first, for everyone’s sake: ALPHAFOLD ISNT AN LLM
That isn’t what alphafold is. Under no circumstances is it anywhere near close to a “database of every way … proteins can fold.” At all. And to construe it as anything other than an attempt at a way to predict or simulate the potential three dimensional structure a protein can adopt will mislead people.
A protein does not have one shape. It has multiple. They’re dynamic. They change shape. It’s how proteins represent information. I’d argue that the ability of proteins to change their shape is one of their most important properties. (Analogy: play a song on an instrument with one note. Hard-mode: consider silence a note)
Everything in Alphafold is a GUESSED MODEL and not reality. Crystal structures and cryo-EM structures are also MODELS. But they’re based on empirical evidence.
Alphafold is based on statistical evidence. It is evidence, but it is weaker. If we don’t have an example of how a protein might fold in the structural database, alphafold will struggle to predict the structure. At least not without it sharing some type of sequence similarity.
I see this in the AI drug companies and how they just treat predictive models the same as 2 angstrom crystal structures and it pisses me off.
Not an expert at all, so thanks for clarifying what the alphafold project is in more detail. My bad on the confusing wording as well, i specifically mentioned my distrust of commodified llms to distinguish that from whatever alphafold and similar projects would be (don’t know if that use of ai has a specific term).
From what I know of the project it seems to be nice use of ai tech, am i wrong in that? Genuinely asking :)