Case & Scenario Application

Basically, when you have a protein sequence with an unknown structure, RAPTOR can predict its structure for you in hours, compared with NMR or X-Ray techniques which are costly and takes several months. Overall, RAPTOR will save you and your lab a lot of time, money and effort. This is especially useful for academic users who want to publish as soon as possible.

The structural information predicted by RAPTOR can be used in many different areas. Here are some examples from our current customers. This is not a full picture about using RAPTOR but it will help to find out how RAPTOR can help your research.

Protein Threading

• Protein Threading is the most fundamental use of RAPTOR for everyday use. When there is marginal sequence homology, your homology search tool (i.e. BLAST) may fail. In that case, you should try RAPTOR. When the sequence homology is low (below 25%), RAPTOR consistently gives a constructive prediction.

Functional Annotation

• This is based on the observation that proteins with similar structures have similar functions. If there is a protein sequence with an unknown structure and you want to know its function, you can run RAPTOR with the sequence. The top template (whose function is already known) returned by RAPTOR is believed to have a similar structure with the query sequence. Consequently, the sequence may have the same function (active site) as the template. For more information about functional annotation, see the RAPTOR Pipeline.

Identifying Putative Distant Relationships

• Suppose you have several protein families that you have already studied thoroughly. Now you want to identify some putative distant members of the protein families. You can create your own template library by making the proteins in your protein families’ templates. After that, you can run RAPTOR to scan the sequence database against your own template library. In this way, you will filter out those sequences that have distant relationships with your protein families.

Secondary Structure Prediction

• RAPTOR uses secondary structure prediction results when threading. When 3D structure prediction has been obtained, RAPTOR’s prediction can be used to help further improve secondary structure prediction accuracy.

Crystallography

• When crystallographers try to obtain X-ray crystallography of a protein, they need to collect as much 3D information as early as possible. The plausible structural template identified by RAPTOR can be used to model the structure of the protein. For example, it can be used in molecular replacement phasing.