Online_DPI: a web server to calculate the diffraction precision index for a protein structure

• Published in: Journal of applied crystallography Vol. 48; no. 3; pp. 939 - 942
• Main Authors: Kumar, K. S. Dinesh, Gurusaran, M., Satheesh, S. N., Radha, P., Pavithra, S., Thulaa Tharshan, K. P. S., Helliwell, John R., Sekar, K.
• Format: Journal Article
• Language: English
• Published: 5 Abbey Square, Chester, Cheshire CH1 2HU, England International Union of Crystallography 01.06.2015; Blackwell Publishing Ltd
• Subjects: Crystal structure; Crystallography; Diffraction; estimated atomic coordinate errors; Molecular structure; protein data bank entries; Protein folding; Software reviews
• ISSN: 1600-5767; 0021-8898; 1600-5767
• DOI: 10.1107/S1600576715006287

An online computing server, Online_DPI (where DPI denotes the diffraction precision index), has been created to calculate the `Cruickshank DPI' value for a given three‐dimensional protein or macromolecular structure. It also estimates the atomic coordinate error for all the atoms available in the structure. It is an easy‐to‐use web server that enables users to visualize the computed values dynamically on the client machine. Users can provide the Protein Data Bank (PDB) identification code or upload the three‐dimensional atomic coordinates from the client machine. The computed DPI value for the structure and the atomic coordinate errors for all the atoms are included in the revised PDB file. Further, users can graphically view the atomic coordinate error along with `temperature factors' (i.e. atomic displacement parameters). In addition, the computing engine is interfaced with an up‐to‐date local copy of the Protein Data Bank. New entries are updated every week, and thus users can access all the structures available in the Protein Data Bank. The computing engine is freely accessible online at http://cluster.physics.iisc.ernet.in/dpi/.