RaptorX is a software and web server for protein structure and function prediction that is free for non-commercial use. RaptorX is among the most popular methods for protein structure prediction. Like other remote homology recognition/protein threading techniques, RaptorX is able to regularly generate reliable protein models when the widely used

PSI-BLAST In bioinformatics, BLAST (basic local alignment search tool) is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLA ...

cannot. However, RaptorX is also significantly different from those profile-based methods (e.g., HHPred and

Phyre2 Phyre and Phyre2 (Protein Homology/AnalogY Recognition Engine; pronounced as 'fire') are free web-based services for protein structure prediction. Phyre is among the most popular methods for protein structure prediction having been cited over 150 ...

) in that RaptorX excels at modeling of protein sequences without a large number of sequence homologs by exploiting structure information. RaptorX Server has been designed to ensure a user-friendly interface for users inexpert in protein structure prediction methods.

Description

The RaptorX project was started in 2008 and RaptorX Server was released to the public in 2011.

Standard usage

After pasting a protein sequence into the RaptorX submission form, a user will typically wait a couple of hours (depending on sequence length) for a prediction to complete. An email is sent to the user together with a link to a web page of results. RaptorX Server currently generates the following results: 3-state and 8-state secondary structure prediction, sequence-template alignment, 3D structure prediction, solvent accessibility prediction, disorder prediction and binding site prediction. The predicted results are displayed to support visual examination. The result files are also available for download. RaptorX Server also produces some confidence scores indicating the quality of the predicted 3D models (in the absence of their corresponding native structures). For example, it produces P-value for relative global quality of a 3D model, GDT (Global Distance Test) and uGDT (unnormalized-GDT) for absolute global quality of a 3D model and per-position

RMSD The root-mean-square deviation (RMSD) or root-mean-square error (RMSE) is a frequently used measure of the differences between values (sample or population values) predicted by a model or an estimator and the values observed. The RMSD represents ...

for absolute local quality at each residue of a 3D model.

Applications and performance

Applications of RaptorX include protein structure prediction, function prediction, protein sequence-structure alignment, evolutionary classification of proteins, guiding

site-directed mutagenesis Site-directed mutagenesis is a molecular biology method that is used to make specific and intentional mutating changes to the DNA sequence of a gene and any gene products. Also called site-specific mutagenesis or oligonucleotide-directed mutagenesi ...

and solving protein crystal structures by

molecular replacement Molecular replacement (or MR) is a method of solving the phase problem in X-ray crystallography. MR relies upon the existence of a previously solved protein structure which is similar to our unknown structure from which the diffraction data is de ...

. In the

CASP Critical Assessment of Structure Prediction (CASP), sometimes called Critical Assessment of Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994. CASP prov ...

9 blind protein structure prediction experiment, RaptorX was ranked 2nd out of about 80 automatic structure prediction servers. RaptorX also generated the best alignments for the 50 hardest

9 TBM(template-based modeling) targets. in

10, RaptorX is the only server group among the top 10 human/server groups for the 15 most difficult

10 TBM targets.

History

RaptorX is the successor to the RAPTOR protein structure prediction system. RAPTOR was designed and developed by Dr. Jinbo Xu and Dr. Ming Li at the University of Waterloo. RaptorX was designed and developed by a research group led by Prof. Jinbo Xu at the Toyota Technological Institute at Chicago.

References

{{Reflist

External links