Protein Structure Property Prediction

RaptorX Property is a web server predicting structure property of a protein sequence without using any template information. It outperforms other servers especially for proteins without close homologs in the Protein Data Bank (PDB) or with very sparse sequence profile. This server employs an emerging machine learning model called DeepCNF (Deep Convolutional Neural Fields) to predict secondary structure (SS), solvent accessibility (ACC), and disorder regions (DISO) simultaneously. DeepCNF not only models complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent property labels. Our experimental results show that this server can obtain ~84% Q3 accuracy for 3-state SS, ~72% Q8 accuracy for 8-state SS, ~66% Q3 accuracy for 3-state solvent accessibility, and ~0.89 Area Under the ROC Curve (AUC) for disorder prediction. RaptorX-Property was ranked 1st in 3-/8-state secondary structure prediction in a third-party evaluation work published in Briefings in Bioinformatics. Software is available here.

Job Identification
: :

Sequences for Prediction      (example)


Current server load
6742 jobs pending
0 jobs done in the last 24 hours
287 jobs done in the last 30 days

#server users: 90397
#processed jobs: 693382

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.
  • Please submit up to 100 protein sequences (in the FASTA format) in a batch for prediction. If your email box cannot receive a large attachment file, please submit a SMALL number of sequences in a batch. Otherwise the result package may be too big to be received.
  • 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.