Take the 2-minute tour ×
Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It's 100% free, no registration required.

Could you show me references of any works you know of where,

1- they take all the known protein structure data (that is the coordinate data of all the proteins in PDB database lets say or elsewhere)

2- then after step 1, make statistical predictions about relations between types of secondary structures (or other geometric data obtainable from coordinates files) in the protein and its function (or other properties of the protein)


share|improve this question

closed as too broad by leonardo, jonsca, Oreotrephes, Amory, GriffinEvo Dec 3 '13 at 9:55

There are either too many possible answers, or good answers would be too long for this format. Please add details to narrow the answer set or to isolate an issue that can be answered in a few paragraphs.If this question can be reworded to fit the rules in the help center, please edit the question.

this is a little broad of a question - RCSB.org has a lot of stats pages. also this sort of sounds like SCOP. scop.mrc-lmb.cam.ac.uk/scop did you mean something more specific? –  shigeta Nov 26 '13 at 14:04
thanks alot for the answer. well I dont really know how to be more specific since it is not my main field now. From my undergraduate I vaguely remember research papers (or references to research papers in book) where they extract coordinate data of a large class of proteins and try to look for re-occuring motifs in a given family of proteins so on and so forth. –  Sina Nov 29 '13 at 16:26
ideally it would be something like we took 10000 proteins` configuration data. we extracted some geometric information about them (could be anything: number and types of secondary structure, number of domains, distance between different types of aa's), looking at this data we inferred some relation between families of proteins/functions of proteins and geometric information that we extracted. I know it is still vague but for now it is the best I can come up with. I am also digging through my old books. (btw: site looks very close to kind of things I am looking for thanks) –  Sina Nov 29 '13 at 16:30

1 Answer 1

the SCOP project did this. scop.mrc-lmb.cam.ac.uk/scop

which far more than 10,000 proteins. their goal was to categorize the protein folds that were known through X-ray and NMR structures. their current status:

38221 PDB Entries. 1 Literature Reference. 110800 Domains. (excluding nucleic acids and theoretical models).

It was last updated in 2009 though.

There is a broad literature where researchers evaluate the geometry of tens of thousands of structures. A review of all of them would be more like a book than an answer to a question on stackexchange!

Their goals range quite broadly; "how does the protein sequence dictate secondary structure?" or quite narrow "how does this specific metabolic enzyme change in structure across many organisms"?

If you can think of something more specific I'll do my best to respond. if you want to know how to do this I can also help with that.

share|improve this answer

Not the answer you're looking for? Browse other questions tagged or ask your own question.