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The ReFOLD server: refinement of 3D models of proteins guided by accurate quality estimates

About the server

The ReFOLD server provides:

  1. Refinement of 3D models of proteins and an assessment of their global quality.
  2. Interactive 3D comparisons of refined and original models
  3. Predictions of the local quality (per-residue error) within multiple refined models.
  4. Machine-readable data downloads

This website is free and open to all users and there is no login requirement.

Fair usage policy:

You are only permitted to have 1 job running at a time for each IP address, so please wait until your previous job completes before submitting further data. If you already have a job running then you will be notified and your uploaded data will be deleted. Once your job has completed your IP address will be unlocked and you will be able to submit new data.

ReFOLD3 server submission form

Help page

Sample output

References

  • Adiyaman, R. & McGuffin, L.J. (2021) ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts. Nucleic Acids Research. gkab300, published online ahead of print. DOI
  • Adiyaman, R. & McGuffin, L.J. (2019) Methods for the Refinement of Protein Structure 3D Models. Int J Mol Sci. 20, 2301. DOI PubMed
  • Shuid, A.N., Kempster, R. & McGuffin, L.J. (2017) ReFOLD: a server for the refinement of 3D models of proteins guided by accurate quality estimates. Nucleic Acids Research, 45, W422-W428, doi: 10.1093/nar/gkx249. PubMed
  • McGuffin, L.J., Shuid, A.N., Kempster, R., Maghrabi, A.H.A., Nealon J.O., Salehe, B.R., Atkins, J.D. & Roche, D.B. (2018) Accurate Template Based Modelling in CASP12 using the IntFOLD4-TS, ModFOLD6 and ReFOLD methods. Proteins: Structure, Function, and Bioinformatics, 86 Suppl 1, 335-344, doi: 10.1002/prot.25360. PubMed


Example of ReFOLD quality assessment guided refinement for CASP target T0892 domain 1. Using ReFOLD we improved upon the initial server model (GDT_TS score improved from 79.71 -> 82.25). Left panel - starting model in cyan, refined model in magenta, actual structure in green. Right panel - GDT plot showing the improvement starting from initial server models (cyan) to the ReFOLD refined models (magenta).

Link to original ReFOLD submission form:

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