RaptorX: Protein Structure and Function Prediction Powered by Deep Learning

RaptorX is developed by Xu group, excelling at secondary, tertiary and contact prediction for protein sequences without close homologs in the Protein Data Bank (PDB). RaptorX predicts protein secondary and tertiary structures, contact and distance map, solvent accessibility, disordered regions, functional annotation and binding sites. RaptorX also assigns confidence scores to predicted structures. See details below and HERE.

Currently the following servers are running. Instructions.
RaptorX Structure Prediction: the main server predicting protein secondary and tertiary structure, binding site and GO annotation. This server is ranked very top in CASPs and the fully-automated, live benchmark CAMEO. See here for a ranking list of the publicly-released structure prediction servers. Please use the RaptorX-Property server if you only want to predict secondary structure, solvent accessibility and disordered regions, and RaptorX-Contact for only ab initio folding and contact prediction.
[Submit][Find jobs by: ID or sequence,Email][Example][Refs: 1,2,3,4]

RaptorX Property Prediction: protein structure property prediction without using templates, including secondary structure, solvent accessibility, and disordered regions. RaptorX-Property was ranked 1st in 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: contact prediction, distance prediction and ab initio protein folding. RaptorX-Contact was officially ranked 1st in contact prediction in both CASP12 and CASP13, the worldwide protein structure prediction competitions. See here for a ranking list of CASP12 participants and the below references for technical details.
[Submit][Find jobs by:ID or sequence,Email][Example][Refs:1,2,3,4,5]

RaptorX Complex Contact Prediction: predicts the interfacial contacts between two potentially interacting protein sequences (heterodimer only) using co-evolution and deep learning techniques.
[Submit][Find jobs by:ID or sequence, Email][Example][Refs: 1, 2, 3]

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
7630 jobs pending
103 jobs done in the last 24 hours
3139 jobs done in the last 30 days

#server users: 64831
#processed jobs: 528655


1. Registration is NOT required, but users are STRONGLY RECOMMEND to provide an email address in submission, which can be used to retrieve the job results. 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, but 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, the higher priority this user has.

2. A job result can be retrieved by the assigned JobID or its sequence or downloaded through My Jobs. The result URL will also be sent to the email address if provided in submission. If you cannot retrieve your jobs results, please 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 (iPAD, Windows 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.