Prediction of natively unstructured regions through contacts
Ucon compared favorably with methods utilizing either one of these approaches alone for proteins with long (>30 residues) unstructured regions. We remained most surprised by the result that methods based on position-specific and position-independent preferences performed similarly on average. A position-independent method only depends on amino acid composition, i.e. is aXXblindaXX to the specific positions in the sequence (e.g. the sequence AGEREG gives the same preference as does REGGAE). Such a simplification obviously ignores the importance of folding pathways that we know matter greatly. The explanation for the minute difference between these two methods might be that there are a great variety of unstructured regions. Some serve as buffering or filling material. These regions just have to be selected to stay clear off binding to anything. Other unstructured regions, in contrast, have strong binding preferences; however, they are selected not to bind internally but to bind through external transient proteinaXXprotein interactions. We provided evidence that our method identified different proteins with unstructured regions than existing methods. Furthermore, we showed that at least for one single example we could specifically identify regions involved in external proteinaXXprotein interactions. Thus, this method might become rather useful for the prediction of protein function, as well as, for more detailed experimental studies of natively unstructured regions.
Installation with aptitude (Debian, Ubuntu, etc.)
- If you have not done so until now, add the rostlab repository to the list of your syanptic package manager. This is how it's done: Debian_repository#sources.list.d
- aptitude update
- aptitude (search for rostlab keyring and install by marking the package with a '+' and hit 'g' twice to install)
- aptitude update (to determine all rostlab packages to install)
- aptitude install ucon. Here's a step by step guide Debian_repository#Installing_a_package_step_by_step
Please see the UCON man page:
This program can be run through the PredictProtein service.