What are the applications of predicting the structure of proteins?

Question

Protein molecules are very important as they are used for catalyzing almost all the chemical reactions in the cell, regulation of gene activity and provide cellular structure.

However, in predicting the structure of protein I haven't been able to find many use cases. In the omicsonline I was able to find a paper on Computational Methods for Protein Structure Prediction and Its Application in Drug Design:

Most modern drug discovery projects start with protein target identification and verification to obtain a verified drug target. For structure-based drug design the three-dimensional structure of the protein needs to be determined experimentally by using either x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy.

Therefore, since proteins are vital for maintaining the body are there any other use causes for predicting the structure?

Answer 1

Just off the top of my head, protein structure is very important for determining how proteins interact, for example determining molecular pathways or viral capsid structures. Knowing the structure of a protein can help scientists better understand what it does and how it does it. By looking at protein structures, scientists can determine exactly how a different allele for a gene causes changes in an organism's phenotype at a biochemical level. Predicting sites within a protein's structure that have an enzymatic function allows scientists to predict how various factors effect it's function. Differences in temperature or pH can have an effect on protein structure as well, and understanding how a proteins changes based on pH or temperature changes can help scientists determine how a protein functions in its specific environment.

Answer 2

To answer your question specifically in the context of drug design: it would of course be great if we could rely on protein structure prediction for drug design, but structure prediction is still not completely accurate. Drug design projects are expensive, so it is often wiser to spend the money on experimental structure determination first, because it will provide a more reliable basis for structure-guided drug design (the alternative would be to spend the money on more failed attempts at designing a good drug, because these attempts are guided by an inaccurate predicted structure).

Also, experimental structure determination is valuable for prediction, because it increases the library of known structures for homology modeling.

Answer 3

protein structure prediction is still in its infancy hence the lack of examples, the benefits are immense however, in proteins structure = function, and as you said proteins catalyze or make up nearly everything in body. We can find out the structure unreliably but predicting the structure would allow us to build proteins to order becasue predicting the structure from sequence means predicting protein folding, which is in many way the holy grail of modern biology. Being able to do it reliably and with more complex proteins would allow us to construct proteins to performs specific tasks instead of hoping to stumble across one that does it then just copying it.