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 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]
Login to your account
Once you submit one job with your email, an account is automatically created for you. Fill in your email address below to see the status of all your jobs.

Server Status
40 jobs pending
133 jobs done in the last 24 hours
4873 jobs done in the last 30 days

#server users: 35921
#processed jobs: 219112


1. Registration is NOT required, but we STRONGLY RECOMMEND you to provide an email address in submission, which can be used to retrieve the results of all your jobs. Jobs can be submitted using a web browser or a command-line program curl. Each user, identified by an email address, can have up to 500 sequences pending prediction at any time point. Jobs are NOT first come, first-served. Instead, they are scheduled to ensure a fair share of the service. A user has the HIGHEST priority if not being served in the past 2 days. The less served a user is in the past 2 days, the higher priority this user has.

2. A job result can be retrieved by the assigned JobID or its sequence. The result URL will also be sent to the email address if provided in submission, which can also be used to retrieve all your jobs through My Jobs. If you lose the JobID or donot receive the email notification (even in your Spam folder), you may contact the RaptorX team by the form.

3. To see the result web page for interactive visualization, your browser shall support HTML5 and allow JavaScript, which is default on most modern browsers such as FireFox, Chrome, IE, Opera and Safari on several platforms (iPAD3, Windows XP and 7 and Mac). To speed up your web browsers, consult here.

News and updates

Top1 In Casp12 Contact Prediction | 2016-12-06 12:36:30

Our RaptorX-Contact was officially ranked 1st in contact prediction in terms of F1 score in the worldwide protein structure prediction (CASP) competition round XII.

System Under Maintenance | 2015-09-30 09:27:50

The computing systems running the servers are under maintenance, so your jobs will be delayed. However, you can still submit new jobs to the servers.

Retrieve Jobs By Their Sequences | 2015-08-12 05:58:42

Sometimes users cannot receive the email notifications upon completion of their jobs due to various reasons. Now users can retrieve jobs by their sequences so that they do not have to keep a record of the job IDs. However, only sequences submitted in the past 60 days can be retrieved since after 60 days it is better to re-predict their sequences, which may result in a better result due to database enlargement.