I am seeking for new research idea about evolution effect on binding site of protein structure (or ligand protein interaction). Is there any place or forum we can discuss about research/project idea?
My background is Physics/Computing. I was criticized by my mentor that I was lost in developing tools and making new figures, but not discovering new science. Then, I think evolution could be a good start point for asking biological question, as evolution is a more global view, which is probably more suitable for Bioinformatics. Or if I cannot find any explanation for the data, probably I can find explanation from evolution. I saw a few papers about using co-evolution to predict relations between proteins inter/intra species. I am kind of wondering whether disease-related gene variances target to the co-evolution sites, or not target to specific sequence location but structurally close.
I am wondering this is a feasible idea, or too hard and small gain in knowledge. I am kind of lost about what biological problems I am trying solve. Should I talk to some structural biologists about what they are interested in?
Another interesting topic for me is how much effect of gene variant (or somatic mutation) to the drug effect.
Not all patients experience the same beneficial drug effects, nor are they equally susceptible to adverse events. Multiple sequence alignment could infer the variability for each base in the sequence. The question I could ask is how much effect these interindividual genetic variances could have on protein ligand binding site? Will a drug be effective for every individual (or a special group of people, like just Caucasian)? How much effective coverage of population could a designed drug have with interindividual genetic variance? With existing pharmacogenetics studies, we can try to understand how genetic differences affect protein-drug interactions and, ultimately, drug response in protein structural level. But, to find adequate data is probably not easy for this project. Or I should focus on a small topic.
I am trying to find a topic which is not too hard and also have some gain in biological knowledge.
Thanks
What your research group works on?
Is there not any follow-up projects?
To arise new idea in the field of evolution and drug dynamics for a PhD student is really challenging, I am also a PhD student that's why I upvoted your post.
There are so much high throughput data available from different species, you just need to have a specific questions to be asked from data. Ideas are like oceans.
This is quite naive idea I have right now , I think I should write it here, just ignore if you think its funny.
For me, the co-evolution of Transcription factor binding sites and sites inside Transcription factors, and the impact of these sites modifications over the regulation and expression. It could be the combined study of DNA-seq, RNA-seq and ChIP-seq. If you find something interesting or unknown, then one way leads to other in Science.
I was working on protein ligand interaction of allosteric effect. However, My two projects are about allosteric ligands, but current papers have already published about allosteric modulator. So, I need to detour a little bit, and find something new. My research group is always interested in drug effect and ligand protein interaction. So I want to extend the scope to include gene variant or evolution. And, the new project must be related to protein structure.
For asking questions, the publication related to that data should have already got most from it.
The sites modification of transcription factor idea, how do you define "the impact"?
So, Impact is.
We know that there are cell-type and species specific competitions between TFs to occupy binding sites.
IF one TF is mutated then its out of race, and then there would be the chance for another TF to bind on that particular region. This would cause some difference in the regulation and expression of the corresponding gene.
Similarly, If binding sites are mutated then it could facilitate the enhancement other TFs affinity.
Genomes accumulate mutations through the series evolutionary consequences.
$0.02 - A subreddit may be not such a bad idea.