Features

Unique Threading Algorithm

• RAPTOR offers three threading algorithms: two based on dynamical programming (DP) and one based on integer programming (IP). The DP algorithms effectively handle most easy sequences (high homology). For hard sequences (low homology), the IP algorithm gives confident prediction.

Supreme Accuracy

• RAPTOR has superior recognition of structure similarities at the fold, family and super family levels. It delivers high accuracy alignments and models, as demonstrated in recent community-wide tests.

Conservation Discovery

• RAPTOR has proven its ability to find structural conservation that is otherwise unnoticed by most threading algorithms. RAPTOR’s unique integer programming algorithm takes pairwise contact potential into consideration when doing threading, which has greatly enhanced the prediction accuracy.

Up-To-Date Template Library

• The structure template library used in RAPTOR is a representative subset of the PDB database. As the PDB is constantly updated, BSI provides template updates every three months.

Easy to Install and Use

• Installation of RAPTOR is fully automated and users just need to specify the installation path. A friendly GUI enables even beginners to start quickly. With the preset configuration, users simply need to click the Run button to obtain final results.

Intuitive Output

• The intuitive output makes it possible to understand relevant data at a glance. E-values enable users to easily judge the significance of the prediction. The color matrix representing sequence profiles help users to easily identify the conservative residues. The colors representing different types of secondary structures in the PIR format alignment allow users to compare the target and template comprehensively. Rasmol is used to help users to examine the predicted structures in 3D space.

Flexible Interface

• RAPTOR works seamlessly and can be configured to call Modeller automatically.

Extensive Platform Support

• RAPTOR supports both Windows and Linux. The latest versions of RAPTOR have been fully tested on Windows XP, 2000 and Vista. For Linux, current versions of RAPTOR have been tested on Fedora and Ubantu.

Parallel Computing

• The threading process is parallelized in RAPTOR. RAPTOR can run in a distributed environment, clusters or on SMP machines, which will substantially reduce run time.