fDETECT - fast Determination of Eligibility of TargEts for CrysTallization

Tutorial and Help | Materials | References | Acknowledgments | Disclaimer | Biomine

fDETECT webserver

fDETECT is a webserver that predicts propensity of protein sequences for completion of material production, purification, crystallization and diffraction-quality crystallization. This webserver implements the fDETECT method - (fast Determination of Eligibility of TargEts for CrysTallization). fDETECT takes less than one second per protein to complete the predictioin.

Please follow the four steps below to make predictions:

1. Choose method to use

2. Copy and paste protein sequence(s) into text area

fDETECT accepts up to 1000 FASTA formatted protein sequences. PPCpred accepts up to 5 FASTA formatted protein sequences. Please enter protein sequence(s) in the following text field (see Tutorial and Help page for details).

3. Provide your email address (required)

Link to the results will be sent to your email address once the results are available. However, the results are also delivered directly via the browser, but please ensure that you do not close or refresh the pages that are displayed after you hit "Run fDETECT".

4. Predict

Click button to launch the predictions. The results are shown in HTML and csv formats. The csv format is easy to parse and you can use our parser written in Python parse_csv.zip. Please refer to the Tutorial and Help page for details.

Materials

The benchmark datasets used to comparatively assess fDETECT:

  • Test_small - Proteins used to evaluate slow and fast methods including fDETECT, PPCpred, Crysalis and PredPPCrys.
  • Test_big - Proteins used to evaluate fast methods including fDETECT and Crysalis.
    The format of these datasets is as follow:
  • line 1: >protein ID from TargetTrack database:one of the four outcomes [Material Production Failed, Purification Failed, Crystallization Failed or Produce Diffraction-quality Crystallization]
  • line 2: protein sequence

References

Upon the usage the users are requested to use the following citations:

Acknowledgments

We acknowledge with thanks the following software used as a part of this server:

  • SEG - Prediction of low complexity regions in protein sequences
  • PSI-BLAST - Finding regions of similarity between protein sequences
  • PSIPRED 3.2 - Prediction of protein secondary structure
  • Real-SPINE 3 - Prediction of residue solvent accessibility of proteins
  • DISOPRED 2 - Prediction of intrinsically disordered regions