For researchers, it is more important to know that software will work in their environment, rather than simply in an ideal scenario. To accommodate users' different needs, RAPTOR supports both Linux and Windows platforms. Alas, there is certainly more than just platforms to be aware of when defining an environment. Here are just a few questions to consider:

• Who in the lab will use the software and how will they interact with it?
• How much detail can be obtained/observed in the results?
• Is the software perpetual/annual?
• Standard License is annual.
• How does one software compare to another, benchmarking?

This section is dedicated to these and other relevant 'Case Use' based issues.

To see a collection of research, produced by users like you and research by BSI, click here.

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.

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.