Protein Contact Map Prediction

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.

RaptorX Contact Predict is a web server that predicts contact map of a protein sequence without using any template information. It applies group graphical lasso (GGL) to contact prediction that integrates joint multi-family evolutionary coupling (EC) analysis and supervised machine learning and works particularly well on proteins without many sequence homologs. Our joint EC analysis is unique in that it not only uses residue coevolution information in the target protein family, but also the residue coevolution information in the related families, which may have divergent sequences but similar folds. Our supervised learning predicts contacts by making use of sequence and sequence profile, contact (distance) potential and other information. Our experimental results show that this server can obtain ~0.92 L/10 accuracy for long-range contacts, and ~0.85 L/10 accuracy for medium-range contacts on 150 protein families used by PSICOV. Finally, the tertiary structure of the input sequence is generated by the aid of predicted contacts, but without using any templates.

Job Identification
: :

Sequence for Prediction      (example)


Current server load
0 jobs pending
177 jobs done in the last 24 hours
3005 jobs done in the last 30 days

#server users: 31292
#processed jobs: 162350

Job policy
To maximize the utility of the server to the community at large the following limits on job submission for each user are enforced.
  • Fill out the form to submit up to 50 protein sequences in a batch for prediction. Sequences shall be in the FASTA format and submitted as a text file or by copy-and pasting into the text field.
  • Please SAVE the assigned JobID for retrieval of job results, especially when an email address is not provided in submission.
  • Each user can have no more than 500 sequences pending prediction at any time.
  • Should you have a special project that requires more resources, please contact us to inquire further.