11 ms·

This is about proteins, not DNA.

by Rochus 6y ago

shawnz 6y ago
Proteins which are coded by DNA.
- Rochus 6y ago
  So what? The DNA only codes for the RNA and amino acid sequence. Structure determination is yet another topic. When we determine the protein structure we already know the sequence. Neither DeepMind has to look at the DNA to train their DNN.
  - shawnz 6y ago
    They are two topics which are both relevant to the discussion. Structure determination is what allows you to see the purpose/effect of the sequence that the DNA encoded.
    - Rochus 6y ago
      Have you read the article? It's about protein structure determination. The DNA only determines the RNA and amino acid sequence. But who cares. I will get a bit less work and citations because http://cara.nmr.ch/doku.php http://cara.nmr.ch/doku.php will be less used in future.
candiodari 6y ago
The full chain is DNA -> mRNA -> Ribosome -> tRNA combinations -> amino acid chain -> protein. It's true that in nature there are many steps between DNA and proteins (this list doesn't even include the steps that mediate the translation, ie. start it, stop it, slow it down, ...), but the structure of a protein is fully determined by the DNA code. Protein folding is about you start from the DNA code that is fed into the ribosome ignoring all the meta information, and come up with an atomic model (VERY long list like "H atom at 3.27,2.17,12.18, C atom at 2.87, 2.19, 12.33, ..."). Now there's a million niceties we've discovered to make this problem simpler and nicer looking, but that's what it boils down to.
- Rochus 6y ago
  Thank you very much; almost forgot I did a Phd on the subject ;-) But anyway your answer does not contradict my statement. What you say belongs to the basics of molecular biology, but does not justify that DNA should be considered when determining the structure of proteins. In practice, the amino acid sequence is always already present.
  - Rochus 6y ago
    For the sceptics: if you read the referenced article, you will see that it is about protein structure determination by means of deep neural networks. It's not about gene expression, which is a different topic. What benefit does it have to respond to the question "What are the immediate real-world applications of this" (see above) by reciting some molecular biology dogmas from text books mixed with misconceptions, instead of responding to the real question?
    - shawnz 6y ago
      Nobody is suggesting that this research has anything to do with gene expression or anything like that. Their point was simply that we now have better tools to actually see the meaning/effect of a given DNA sequence. Also, there is no need to passive-agressively highlight your credentials. I already researched them before replying.
      - Rochus 6y ago
        I rather think most people comment without even having a look at the referenced article. And since when is the reference to a qualification considered aggressive? If your doctor hangs his doctor's certificate on the wall, is he "passive-aggressive"? Pretty weird. > that we now have better tools to actually see the meaning/effect of a given DNA sequence Note that the "meaning/effect" of a DNA segment encoding a protein is known and unrelated to the protein folding process. The protein gets its conformation after the translation process.
        deleted 6y ago

This is about proteins, not DNA.

by Rochus 6y ago

This is about proteins, not DNA.

shawnz 6y ago

Proteins which are coded by DNA.

Rochus 6y ago
So what? The DNA only codes for the RNA and amino acid sequence. Structure determination is yet another topic. When we determine the protein structure we already know the sequence. Neither DeepMind has to look at the DNA to train their DNN.
- shawnz 6y ago
  They are two topics which are both relevant to the discussion. Structure determination is what allows you to see the purpose/effect of the sequence that the DNA encoded.
  - Rochus 6y ago
    Have you read the article? It's about protein structure determination. The DNA only determines the RNA and amino acid sequence. But who cares. I will get a bit less work and citations because http://cara.nmr.ch/doku.php http://cara.nmr.ch/doku.php will be less used in future.

candiodari 6y ago

The full chain is DNA -> mRNA -> Ribosome -> tRNA combinations -> amino acid chain -> protein. It's true that in nature there are many steps between DNA and proteins (this list doesn't even include the steps that mediate the translation, ie. start it, stop it, slow it down, ...), but the structure of a protein is fully determined by the DNA code. Protein folding is about you start from the DNA code that is fed into the ribosome ignoring all the meta information, and come up with an atomic model (VERY long list like "H atom at 3.27,2.17,12.18, C atom at 2.87, 2.19, 12.33, ..."). Now there's a million niceties we've discovered to make this problem simpler and nicer looking, but that's what it boils down to.

Rochus 6y ago
Thank you very much; almost forgot I did a Phd on the subject ;-) But anyway your answer does not contradict my statement. What you say belongs to the basics of molecular biology, but does not justify that DNA should be considered when determining the structure of proteins. In practice, the amino acid sequence is always already present.
- Rochus 6y ago
  For the sceptics: if you read the referenced article, you will see that it is about protein structure determination by means of deep neural networks. It's not about gene expression, which is a different topic. What benefit does it have to respond to the question "What are the immediate real-world applications of this" (see above) by reciting some molecular biology dogmas from text books mixed with misconceptions, instead of responding to the real question?
  - shawnz 6y ago
    Nobody is suggesting that this research has anything to do with gene expression or anything like that. Their point was simply that we now have better tools to actually see the meaning/effect of a given DNA sequence. Also, there is no need to passive-agressively highlight your credentials. I already researched them before replying.
    - Rochus 6y ago
      I rather think most people comment without even having a look at the referenced article. And since when is the reference to a qualification considered aggressive? If your doctor hangs his doctor's certificate on the wall, is he "passive-aggressive"? Pretty weird. > that we now have better tools to actually see the meaning/effect of a given DNA sequence Note that the "meaning/effect" of a DNA segment encoding a protein is known and unrelated to the protein folding process. The protein gets its conformation after the translation process.
      - deleted 6y ago