Starting Aug. 16, 2025 at 9:00 AM (Eastern Standard Time), this server will be shut down temporarily to migrate services to our new server at https://colmar.cloud. Please update your bookmarks accordingly.

All saved user jobs, files, and settings will be migrated automatically. The new server will be fully operational by Aug. 18, 2025.

This current server will remain accessible until Aug. 31, 2025. However, any jobs submitted after Aug. 16, 2025 at 9:00 AM (EST) will NOT be migrated to the new server.

Web server for the prediction of protein loop timescales, NMR S² order parameters, and B-Factors from a single protein structure

This web server predicts motional amplitudes and timescales of proteins from an average protein structure (PDB) as input. The web server returns crystallogragphic B-factors for all heavy atoms, backbone N-H and side-chain methyl (CH3) group S² order parameters, and the dynamic timescales of every protein loop denoted as fast, slow, or static. It provide both intuitive visualization and result download.

The input PDB file can not have any missing residue or heavy atom.

Visualization of the results may not work properly for PDB with multiple chains (to be solved later).

Reference

• Yina Gu, Da-Wei Li and R. Brüschweiler; Decoding the Mobility and Time Scales of Protein Loops; J. Chem. Theory Comput.; 11,1308-1314 (2015);

• F. Zhang and R. Brüschweiler Contact model for the prediction of NMR N-H order parameters in globular proteins J. Am. Chem. Soc 124, 12654-12655 (2002)

• D. Ming and R. Brüschweiler Prediction of methyl-side chain dynamics in proteins J. Biomol. NMR 29, 363-368 (2004)

• Da-Wei Li and Rafael Brüschweiler All-atom contact model for understanding protein dynamics from crystallographic B-factors Biophys J. 96, 3074-3081 (2009)

Questions or comments? Please feel free to contact us.

Acknowledgement

This web server and the research that led to it is supported by the National Science Foundation (Grants No. MCB-0211512, MCB-0507444, MCB-0621482, and MCB-0918362).

*This information is only used for the compilation of our webserver usage data.

This server is last updated at September 14 2024 11:34:33.

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