Protein Structure Prediction
RaptorX is a protein structure prediction server developed by Xu group, excelling at predicting 3D structures for protein sequences without close homologs in the Protein Data Bank (PDB). Given an input sequence, RaptorX predicts its secondary and tertiary structures as well as solvent accessibility and disordered regions. RaptorX also assigns the following confidence scores to indicate the quality of a predicted 3D model: P-value for the relative global quality, GDT (global distance test) and uGDT (un-normalized GDT) for the absolute global quality, and RMSD for the absolute local quality of each residue in the model. RaptorX-Binding is a web server that predicts the binding sites of a protein sequence, based upon the predicted 3D model by RaptorX. More details can be found here: http://raptorx.uchicago.edu/about/
- Currently, we have the following three servers available.
- RaptorX - protein structure prediction
- [Submit] [Home]
- RaptorX new version in beta - see the box below
- [Submit] [Home]
- RaptorX-Binding - model-assisted protein binding site prediction
- [Submit] [Retrieve Results by JobID]
Results from all three severs are retrievable by user's email. RaptorX-Binding results can also be accessed using the provided JobID.
We recomend using Google Chrome or Firefox to view the prediction results due to incompatibility issues with the latest version of IE. Java needs to be enabled in your browser to see the results. For help with Java setup, consult http://java.com/en/download/help/enable_browser.xml
The new version of our RaptorX Server is now in Beta and open for use at http://raptorx.uchicago.edu/StructurePrediction/predict/. Both versions will be available until the end of April and users can submit sequences to either server. After this period the job submission will no longer be available on the old server. However, all previous job results will remain accessible.
We would like to emphasise that the new server is better in prediction accuracy and provides both local and global model quality scores: P-value for relative global quality, uGDT/GDT for absolute global quality and local RMSD for absolute local quality at each residue. The new server is also different from the old one in that it merges the domains sharing the same template into a single model while the old one does not.
News and updates
We are going to upgrade the RaptorX server by the end of Feb 2013. This upgrade includes a much better alignment and modeling algorithm and also a better user interface.
A new version of the standalone threading program is available for download at http://raptorx.uchicago.edu/download/. This version is much more robust, efficient and also user-friendly than previous ones. If you need to predict structures for many sequences, you may install this standalone program locally. However, our web server does provide more functional modules and also visualization of the results.
Recently some users submitted very long sequences to RaptorX, so you may have to wait for a longer time than usual to receive result notifications. We are working on a new version of RaptorX, which shall have a much better throughput.
