Disclaimer: I'm a co-author of one of meta-server methods.
Karsten Suhre [karsten.suhre@igs.cnrs-mrs.fr] wrote: > > before attacking an alignment by hand, I would try some more sophisticated > alignment programs, i.e. those that can include structure information.
This is true and tcoffee is highly recommended but please do not recommend a single threading-based methods on their own to newcomers.
No single structure prediction method is able to match performance of combined approach which includes following steps:
- target protein class discovery - prediction of primary (family membership) and secondary structure (including disordered regions) - structure prediction itself - approaching the consensus
I highly appreciate Fugue method as such but what was outlined above should be kept in mind.
Of course in a simple cases a 'naive' structural alignment, for example produced by tcoffe in a structural mode might be just in case.
Cheers,