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.
[Submit] [Find jobs by: ID or sequence, Email] [Example] [Refs: 1, 2, 3, 4] [Home]


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.
[Submit] [Find jobs by: ID or sequence, Email] [Example] [Refs: 1, 2, 3] [Software Download]


RaptorX Contact Prediction: predict contact map of a protein sequence and tertiary structure guided by predicted contacts, but without using any templates.
[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
0 jobs pending
9 jobs done in the last 24 hours
513 jobs done in the last 30 days

#server users: 15512
#processed jobs: 85604



Instructions:

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

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.