Autodep 4.1: a web-based deposition and archival system
S. Sen, Glen van Ginkel, Adamandia Kapopoulou, G. Sahni, Ganesh Jawahar Swaminathan, R. H. Newman, S. Velankar, K. Henrick · Acta Crystallographica Section A Foundations of Crystallography · 2007
The Macromolecular Structure Database (MSD) (http://www.ebi.ac.uk/msd/) [1] group is one of the four partners in the worldwide Protein Data Bank (wwPDB) [2], the consortium entrusted with the collation, maintenance and distribution of the global repository of macromolecular structure data.Structures can be deposited at the MSD using the AutoDep [3] deposition tool or with the other wwPDB partners using the ADIT system.The AutoDep 4.1 is an extension of the previously developed software AutoDep 4.0 [4], [5] which was a complete rewrite of the original AutoDep system.The AutoDep system allows value-added information to be returned in a safe and secure manner into the passwordprotected deposition session only accessible to the depositor, following annotation of the structure by curation staff, within 2 days of deposition.AutoDep 4.1 is also available for download and installation in-house, where a deposition can be completed and validated before uploading the whole deposition session to the MSD site, where submission to the wwPDB can be completed in minutes.The extended version of AutoDep (4.1) provides detailed information regarding the ligand binding sites, Uniprot sequence mapping and taxonomy information, applets for viewing the files, in addition to structure factor validation statistics, quaternary structure assessments, and new ligand dictionaries.With structures being determined at an ever increasing rate, it is imperative that deposition tools keep pace with this exponential growth of data.We believe that the latest release of AutoDep has significantly automated the deposition process, reduced the time taken to deposit a structure, and at the same time harnessed services offered by the MSD group in returning useful information to the depositor.