RaptorX: Protein Structure and Function Prediction Powered by Deep Learning

RaptorX is developed by Xu group, excelling at 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.

The first web server is currently overloaded and the waiting time is 2-3 days per protein. That is, if you submit 10 proteins to fold, you will have to wait for 20-30 days to get all of them done since our server uses a round robin job scheudling strategy. So if you have quite a few protein sequences to fold and have at least one GPU and a reasonable number of CPUs, you may install our standalone software package on your own machines. Due to limit of computing power, currently side-chain packing is turned off. We will turn on this soon. See our manuscript for the latest result of this server.

Currently the following servers are running. Instructions.
RaptorX Structure Prediction: distance-based protein folding powered by deep learning. This server was officially ranked 1st in contact prediction in both CASP12 and CASP13 and initiated the revolution of protein structure prediction by deep learning. In addition to 3D models, this server also provides inter-residue/inter-atom distance and orientation probability distribution that may be used by other folding algorithms to rebuild protein 3D models.
[Submit][Find jobs by:ID or sequence,Email][Example][Refs: 1, 2,3,4,5,6]


Old Structure Prediction Server: template-based protein structure modeling server. If you know that your sequences have close homologs in PDB, this server is a good choice. Otherwise, please use the above server. This server also predicts protein secondary structure, binding site and GO annotation. Please use the below RaptorX-Property server, which is very fast, if you only want to predict secondary structure, solvent accessibility and disordered regions.
[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 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
426 jobs pending
291 jobs done in the last 24 hours
7146 jobs done in the last 30 days

#server users: 69250
#processed jobs: 559082



Instructions:

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.