RaptorX: a Web Portal for Protein Structure and Function Prediction
This web portal for protein structure and function prediction is developed by Xu group, excelling at secondary, tertiary and contact prediction for protein sequences without close homologs in the Protein Data Bank (PDB). Given a protein sequence, RaptorX predicts its secondary and tertiary structures as well as contact map, solvent accessibility, disordered regions and binding sites. RaptorX 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 predicts the binding sites of a protein sequence, based upon the predicted 3D model by RaptorX. More details can be found HERE.
- Currently, this web portal is running the following servers.
- RaptorX Structure Prediction: predict tertiary structure of a protein sequence using templates. This shall be the main server for tertiary structure prediction. For only secondary structure, please use the Property Prediction server, which is much faster. This server is ranked 1st in the past 3 months in the fully-automated blind test CAMEO. See here for a ranking list of the publicly-released structure prediction servers.
- [Submit][Find jobs by: ID or sequence,Email][Example][Refs: 1,2,3,4]
- RaptorX Property Prediction: predict structure properties of a protein sequence without using templates, including 3-/8-state secondary structure, solvent accessibility, and disordered regions. For tertiary structure, please use the Structure Predicton server. Our RaptorX-Property was ranked 1st in 3-/8-state secondary structure prediction in a third-party evaluation work published in Briefings in Bioinformatics.
- [Submit][Find jobs by:ID or sequence,Email][Example][Refs:1,2,3,4][Software Download]
- RaptorX Contact Prediction: predict contact map of a protein sequence and tertiary structure guided by predicted contacts, but without using any templates. Our RaptorX-Contact was officially ranked 1st in contact prediction in terms of the total F1 score in the worldwide protein structure prediction (CASP) competition round XII. See here for a ranking list and our paper for technical details.
- [Submit][Find jobs by:ID or sequence,Email][Example][Refs:1,2,3]
- RaptorX Binding Prediction: model-assisted binding site prediction for a protein sequence.
- [Submit][Find jobs by:ID or sequence,Email][Example][Refs]
- RaptorX Structure Alignment: align two or multiple protein structures.
- [Submit][Retrieve Results by JobID][Example][Refs: 1,2][Software Download]