Modifying Existing Approach In Protein Structure Research Area

Question

[GreenDiamond]

Hello,

I have a very open-ended class project, where I should-

• Review and summarize one research area
• Propose a new approach to an existing one
• Implement the proposed approach

The topic can be on things like-

• Protein geometry
• Identification of domains
• Secondary structure prediction
• Tertiary structure prediction
• Protein-protein interaction
• Protein structure alignment

The project should be small and specific (for someone with very little experience to complete in a short time frame). Being able to easily access an existing approach and modify it is the goal. The problem is, I am unfamiliar with these fields, and having a hard time trying to find something doable with my limited background for this specification.

Any suggestions greatly appreciated!

** This message was edited from its original post

[Istvan Albert]

this is a question that cannot be answered as stated, too open ended

[GreenDiamond]

I agree it is probably difficult to answer; I am not asking for a tangible code or numerical solution to a math problem. I am not sure how to make it less open-ended though. Basically, I have a project idea (comparing sequence percent identity with RMSD calculations - once for Ca atoms only, once for all atoms). But, I worry whether or not this has any significance in proteomics, and/or if the problem could be tweaked to ask a question that someone knowledgable about current proteomics could suggest to me. Thanks.

[Istvan Albert]

allright, I will suggest to remove the other information, of how long the project should take, etc those feel a bit distracting

I would rework the title and focus on just the question which is basically prior work/tools on using the percent identity to determine protein structure

[GreenDiamond]

Thanks Istvan. I changed the title and the post, actually, to fit what the specifications have been broadened to! I tried to make it more clear. I wanted to include the information about time-frame, because it really does need to be a small project that could be complete in 5 weeks. I was worried readers would think it was a project without a deadline!

Answer 1

[Woa]

CA-CB distance has been use previosly so far I can remember. You can think about some 'alternative' distance meaures which can better capture the differences between the two proteins other than RMSD. People have proposed some modified RMSD measures.

BTW there can be extremely similar structures with extremely poor sequence similarity

[GreenDiamond]

Thanks Woa. I saw that there are global distance tests and other measures, besides RMSD. I updated the project specifications to be more clear. (Because that is above my head right now; I don't think I could complete a new measure to improve upon RMSD with my limited skills!)

Answer 2

[João Rodrigues]

The reason of incorporating side-chains is not necessarily because of similarity, but it might be depending on the question you want to answer. Also, like Woa mentioned, you can have totally different proteins with the same fold, or vice-versa.

I don't know what kind of project it is, theoretical or practical, but you could for example benchmark which algorithm for alignment performs better (i.e. faster and more precise) and then implement it in a tool that allows very easy manipulation of which atoms to include in the calculation, which zones of the protein, optimization cycles, etc, etc. I think this could be done in 5 weeks and it would be a fun project to learn from and also useful in general. Have a look at Profit, something like this, but much more efficient would be nice!

[GreenDiamond]

Thank you for the Profit link, Joao. I updated my post to be more clear about the project. Apparently, it does not have to be limited to structural alignment/RMSD. If you have any other suggestions, I would love to hear them! By the way, I have very little experience in this field and my teacher knows that, so the project can be very small. Thanks again!

[João Rodrigues]

How long do you have?

[GreenDiamond]

Thanks. I still only have ~5 weeks. And this project is for one course of several, so it will not be my entire focus day in, day out. Maybe a 2 hours a day.