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A related question I always had: how much does computational tools really help in the biochemistry as a whole given the tons of variables that we just can't eve
by up6w6 5y ago
A related question I always had: how much does computational tools really help in the biochemistry as a whole given the tons of variables that we just can't even measure perfectly ? As a computer scientist I can see how rigid data structure algorithms are useful in dna sequencing but I'm not aware of how useful is a simulation of some metabolic pathway for example.
- pfisherman 5y agoComputational tools are insanely helpful and wifey used in biotech. Generally you see them spring up around experimental platforms (ex gene / RNA sequencing). In terms of your particular example, how good is your simulation? If your simulation can accurately predict the effects of perturbations on metabolic pathways, then PM me and we can start a biopharma company.
- up6w6 5y agoIt's exactly what I'm asking, what is the status of our current metabolic pathway simulations for example ? how much about protein denaturation do we need to know before protein structure prediction is useful ?
- pfisherman 5y ago> how much about protein denaturation do we need to know before protein structure prediction is useful ? Denaturation is not all that significant. Physiological conditions (i.e. pH, temperature, etc) tend to be maintained by homeostasis. Protein structure prediction is already incredibly useful. > what is the status of our current metabolic pathway simulations for example ? IMO we do not have the data to build useful metabolic pathway simulations. To do a good simulation you need to know (1) the proteins and metabolites involved, (2) their functions and key biophysical properties (ex. Km), (3) feedback / control elements. For most pathways we do not have (1). The data for (2) are mostly nonexistent, buried in literature, and / or unreliable. Same with (3).