Protein Structure and Function 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.

Currently, we have the following servers available.
RaptorX structure prediction - 3-state and 8-state secondary structure, solvent accessibility, disordered regions and tertiary structure prediction for a sequence
[Submit] [Retrieve Results by JobID] [Home] [Example] [Refs]

RaptorX-Binding - model-assisted protein binding site prediction for a sequence
[Submit] [Retrieve Results by JobID] [Example]

RaptorX Contact Prediction - protein residue contact prediction for a sequence
[Submit] [Retrieve Results by JobID] [Example] [Refs] [Software Download]

RaptorX Structure Alignment - protein pairwise and/or multiple structure alignment
[Submit] [Retrieve Results by JobID] [Example] [Refs] [Software Download]
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Server Status
88 jobs pending
158 jobs finished in the last 24 hours


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. The result URL will be sent to the email address 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

Contact Server Suspended | 2015-01-31 19:42:06

The server machine running the contact server jobs has a dead hard drive. We will have to install a new hard drive, the operating systems and all the code needed for the contact server, which will take at least one week. However, users can still submit their contact prediction jobs and access the results of previous jobs.

Contact Server Impacted | 2015-01-28 17:52:01

Our system is under upgrade and the contact prediction jobs submitted in the past few days are impacted and delayed. We will run all the pending contact jobs as soon as we have finished the system upgrade.

Error In Connecting To Server | 2014-10-02 21:40:08

Some users may see an error message in connecting to RaptorX. This is due to mis-configuration of our Firewall system. We will fix the problem as soon as possible.