New answers tagged structural-biology
TLDR; Answer: You could consider this particular residue to belong to both structural elements, but it's a tricky call and depends on the method of secondary structure assignment. Ambiguous secondary structure allocation comes up fairly often. Whilst obviously, not many people will be able to use this protein specifically, the below approach could be ...
You can also search for amino acid sequences directly at the PDB repository.
One way of doing this is to run a protein BLAST search at NCBI in which you specify the Protein Data Bank as your database, as in the example shown below: The results will be all for proteins in the PDB.
the OH group in the two position acts a as a nucleophilic catalyst for the cleavage of RNA or of DNA if it had such a group. Since DNA needs to stay intact throughout the life of a cell it would be disastrous if it were cleaved because of the 2'OH group. RNA on the other hand is rapidly cleaved as needed by the cell without detrimental consequences to the ...
If you are only looking for secondary structure prediction you could try the JPred-server API. On their website they refer to a script that provides a JPred user with advanced functionality for an easy submission of hundreds of JPred jobs in a sustainable manner. […] For full details on the code, how-to, and for download please check Fabian's GitHub ...
The fact that there is no inter-strand cross-linking between different double strands might be just because the cross-linker cannot bridge the distance between amines of different bases on different double strands. The formaldehyde based linking of nucleobases has been described by Chaw et al. (1980) where formaldehyde bridged a gap of app. 3 angstroms (2x ...
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