Determining protein structure and function from cDNA?

[drairways]

protein structure and function?
Hey guys....

I was just wondering, if i had obtained the nucleotide sequence of a novel cDNA clone, how could i use the web-based sequence analysis to make predictions about the structure and function of the protein???

Plus if i assumed that the protein which i found was a new member of an existing protein family, how could i go about identifying potential important amino acids in the sequence?


Cheers.... thanks a million
Thanks
DR

[JackBean]

You're lucky one

Use BLAST (like the one on www.pubmed.com ) to find similar sequences, it also searches for domains, so even if you won't find anything really similar, the domains can help. But anyway, if it finds some highly similar sequences, you can assume, that your protein has the same function.
For searching for important aminoacids, use multiple alignment like ClustalW here
http://www.ebi.ac.uk/Tools/clustalw2/
with several proteins with the same putative function. The more proteins, the better, because when you use like 5 proteins, many and many AAs will look like conserved, but that's only small example, only if sing many proteins, you will see only the really conserved AAs (those, which are really important, like in active site).
For structure determination, NMR or X-rays are the best choice But for PC modeling I suggest HHpred
http://toolkit.tuebingen.mpg.de/hhpred
or there is also FeatureMap3D at CBS department of Danmarks Tekniske Universitet
http://www.cbs.dtu.dk/services/FeatureMap3D/
If these won't find any homologous protein with structure, you can do modelling de novo, but as you are asking, what to do at all, I do not recommend that