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The redox responses of the complexes confirmed the submitted structure of the complexes.
By the mid 1990s, the editorial office had a system for assembling a validation report of a submitted structure based on the output from several crystallographic applications that were by then able to read CIF directly [19].
The applet converts and stores the submitted structure into a temporary SDF format on the host server.
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81859 alignment results were obtained from the 3179 submitted structures.
It also allows to dynamically handle any new user submitted structures.
Others provide comparison of entire protein structures (Ausiello et al., 2008) against a number of user submitted structures.
These results show that PDB_REDO can also improve the most recently submitted structures and that current day depositors can benefit from using PDB_REDO pipeline to improve a structure model before it is submitted to the PDB (see for example Peng et al., 2010).
To find out the structure of the closest related proteins we submitted the structure to the NCBI protein BLAST tool and performed BLAST against the Protein Database (PDB).
Then to detect correction for the residue of prediction MX2 structure, we submit the structure to rampage Ramachandran (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php).php
We also submitted our structures to the RCSB ADIT structure validation tool which outputs a full report on the structure including RMSD values for covalent bonds and angles relative to standard values for nucleotides (Clowney et al., 1996; Gelbin et al., 1996).
We then submitted this structure (only the backbone atoms) to the SWCRL program for prediction of side-chain conformations [38].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com