I just watched this video https://youtu.be/gVzPMZqOTo4 and was wondering how long folding at home will stay relevant. Aren't we wasting a lot of power if a neural network can perform the same task in a fraction of the time?
Hi everybody!
My question is not about the definitions of these words, but if you consider using it as a starting point, I leave you with the vague definitions about the the words organic and inorganic:
Inorganic: relating to or denoting compounds which are not organic (broadly, compounds not containing carbon). -from Oxford Languages
Organic: relating to or denoting compounds containing carbon (other than simple binary compounds and salts) and chiefly or ultimately of biological origin. -from Oxford Languages
Inorganic Compound: "...However, the distinction is not clearly defined; authorities have differing views on the subject." -from Wikipedia
I gave these examples because the introduction of customized definitions before understanding well how main principles of chemistry works makes it difficult for the learner to understand with the whole context. (IMHO)
I wanted to point this out because I'm trying to understand the working principles of chemistry, not the next-stage definitions that branched out into specialties.
Thanks a lot for the replies!
I understand that when protein is in primary/secondary structure there is more organization of water molecules, hence it has low entropy and when you fold it, the entropy of protein increases but the entropy of water (which becomes more positive) overcomes the entropy of folded protein. I know that proteins like hydrophobic parts inside and hydrophilic outside and that's what's confusing me. If hydrophilic residues are outside, wouldn't that interact with water and make water more organized?
After reading immune and looking into details about AlphaFold, I am curious to learn more about protein folding. Can we have a video on protein folding with a small section explaining Levinthal's paradox?
I’m trying to start fold@home for banano. I was wondering if anyone could point be in the direction of what computer to buy to generate the most bananos and fold the most proteins per day?
Also, anyone care to share how much banano they earn per day with their specs?
Hi. I hope this topic is apporpriate for this sub. I come from a Physics/Fluids Engineering background and I stumbled across a video about protein folding 2 years ago that really got into my mind. Since then, I've been passively reading about protein folding, molecular dynamics and deep learning. I would like to take a step towards more active learning about protein folding, but my academic background is so different from the area that I struggle even to define keywords to look for content related to the fundamentals of protein folding. My hint is that I should look for Cell Biology content. How should someone from a different area approach this subject?
Thanks, everyone!
After having a very hard time grasping the biology domain knowledge, I am very proud to share my biology summaries. We tried to create a self-complete guide for ML engineers-researchers with zero background on biology. If you aim is to understand protein folding and alpha fold check out our blogpost:
https://theaisummer.com/deep-learning-biology-alphafold/
We also talk about ML design and knowledge of the data, here proteins.
Contents:
- The central dogma of biology
- Proteins and protein levels
- Amino acids, nucleotides and codons
- Protein structure characteristics such as Domains, Motifs, Residues and Turns
- Distograms
- Phenotypes and genotypes
- Multiple sequence alignment
- Biology tasks that can be approached with ML
- Association of biology and ML model design
Let me know of your thoughts!
Cheers,
Nikolas
I understand that the secondary structure of a protein consists primarily of alpha helices and beta-pleated sheets. But various resources state that certain amino acids tend to form certain alpha helices/beta pleated sheets. If secondary structure depends on the bonds between the amino acid backbone, does the R-group matter here?
I think I’m also getting confused with what proteins really look like. They still keep those alpha helices/beta sheets in tertiary structure too, right?
in protein folding, is backbone and amino acid chain the same thing?
