RAPTOR Versions Page

RAPTOR (RApid Protein Threading PredictOR) was created from research in automated protein prediction. The first versions did not have a GUI (graphical user interface) and could only except command line input and commands. From that humble beginning RAPTOR has grown into a user friendly program that is intuitive and easy to learn.

RAPTOR Versions

RAPTOR 4.5 - Released February 8, 2010

RAPTOR 4.4 - Released August 15, 2009

RAPTOR 4.3 - Released February 25, 2009

RAPTOR 4.2 - Released November 1, 2008

RAPTOR 4.1 - Released May 1, 2007

RAPTOR 4.0 - Released September 6, 2006

RAPTOR 3.1 - Released January 1, 2006

RAPTOR 3.0 - Released July 6, 2005

RAPTOR 2.0 - Released August 15, 2003

RAPTOR 4.5

• New GUI for easier navigation
• Project oriented work flow
• Greater detail provided about alignments in tabular format
• More options to run OWL/Modeller on alignments from ranking list
• Project organization for importing PIR files before running OWL/Modeller
• Independant project management control. One sequence per project.

RAPTOR 4.4

• Support alignment file (in PIR format) as an input file. RAPTOR parses the pir file, extracts the sequence from it and displays the alignment in the ranking list in a separate group.
• 3D structures can be predicted on any alignment from the ranking list by selecting it and sending it to OWL.

RAPTOR 4.3

• An improved ranking algorithm that proved very effective in recent CASP8, resulting in top rankings across all servers.
• New secured licensing module with user friendly registration wizard that makes registration process easy.

RAPTOR 4.2

• The major contributions to this release include an internally provided structure modelling tool (OWL), specially created to maximize RAPTOR output.
• Threading algorithm enhancements have proven successful in CASP8, resulting in the top ranking of commercial protein structure prediction software.
• Lastly, a completely user intuitive interface allows greater flexibility.

RAPTOR 4.1

• Armed with unique integer programming algorithm, RAPTOR is capable of discovering remote structural homology for hard sequences and giving high quality prediction. As a participant in recent CASP's, RAPTOR has been consistently ranked in the top tier. In addition to the three threading methods proprietary to RAPTOR, the new version integrates PSI-BLAST for rapid identification of easy targets. A built in pipeline in RAPTOR 4.1 allows users to automatically run more rigorous threading techniques if necessary. RAPTOR 4.1 is your protein structure pipeline, right out of the box.

RAPTOR 4.0

Same effort, Even better output.

• RAPTOR 4.0 is a totally new GUI, which looks much better than RAPTOR 3.0 and much easier for users to use. The configuration panel helps you to set up RAPTOR in a few seconds. With RAPTOR 4.0, you can run the three different threading methods one by one which will save much time. By working seamlessly with Modeller, this software is able to produce ICM Pro input files. The color scheme used to visualize the output makes it very intuitive for users to understand threading output. The output table ranked by E-values allows users to view all the information about a template in one window. Users can compare alignments from different methods, line by line in the same window. The size of the RAPTOR 4.0 package is more compact than RAPTOR 3.0, reduced from several Gigabytes to just one Gigabyte.

New features

• Unique Threading Algorithm
3 threading methods, each with unique integer programming techniques
• Supreme Accuracy
Superior recognition of protein similarities at the fold, family and super family levels.
• Conservation Discovery
Proven ability to find conservation, otherwise unnoticed
• Propriety Template Creation
Generates templates from proprietary PDB files
• Up-to-date Template Library
Threading engines using latest PDB-derived template library
• Easy-To-Use
Friendly GUI enables beginners to start running a sequence in 1 minute
Flexible interface
Works seamlessly with Modeller
Exports ICM PRO compatible files
• Parallel Computing
Runs in a distributed environment and on SMP machines

RAPTOR 3.1

New features

• RAPTOR 3.1 has redesigned configuration panel. It will become more easy to use for beginners and also more convenient for advanced users.
• PSI-blast uses RefSeq sequence database instead of the large NCBI NR database used in version 3.0. This will dramatically increase the speed of analysis without significant loss in accuracy.
• RAPTOR 3.1 allows users to run the same sequence multiple times under different methods without data being over written.
• The XML analysis output for multiple runs of the same sequence is now grouped in one convenient file.
• Any reported bugs in the 3.0 version have been fixed for the 3.1 version.

Please note: The features included in the final version may be different then those listed above.

RAPTOR 3.0

New features

The following new features have been incorporated with 3.0:

• We have incorporate eValues into our results to give our users a better feel for what the results mean. SVM scores are still available for our client who fine them more useful.
Choose the method that suits your data!
• Three threading methods are available to use; IP, NP, No Core.

Interface enhancements

The following enhancements to the user interface have been made for 3.0:

• RAPTOR now has a GUI (Graphical User Interface) that allows users to easily control the tool and view results.
RAPTOR is easier than ever to use!
• The results are outputted to HTML.

Compatibility with earlier versions

RAPTOR 3.0's data results are not compatible with version 2.0 or lower. The command line interface is not longer supported in this version.

RAPTOR 2.0

New features

The following new features have been incorporated with 2.0:

• Outputs to XML format for easy extraction processing and analysis.
• Both secondary structure and profiling information are incorporated in the threading process.
• Generate protein templates from proprietary PDB (Protein DataBase) files.
• Ability to rank templates candidate by user-specified scores (SVM, raw, z-score)
• Now runs in a distributed environment and on SMP (Symmetric Multi-processing) machines.
• Interactive command line interface that enables batch mode processing.
• Window2000/XP and MAC OS X versions available.