5 structural search engines – who are your protein’s neighbors?
It is well known that proteins that share high sequence identity usually share the same fold and approximately the same structure, this is the basis for homology modeling. It also well known that some folds contains proteins with very different sequences. These cases pose a problem for sequence based structural alignments and for sequence based search protocols. For that reason, algorithms were devised to quickly and efficiently search (let’s say – the entire PDB) for proteins with a similar structure although not necessarily with similar sequence.
We present a list of 5 such algorithms, implemented into a publicly available web-server, for your convenience (some are even available for download). These software relay on sophisticated superposition algorithms and hence you can use most of them to just accurately superimpose two structures.
