Deposit3D: a tool for automating structure depositions to the Protein Data Bank

Journal Article · Thu Sep 01 04:00:00 EDT 2005 · Acta Crystallographica. Section F

DOI:https://doi.org/10.1107/S1744309105026126· OSTI ID:22356163

Hendle, J.; Burley, S. K.; Kissinger, C. R. ^[1]

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1. SGX Inc., 10505 Roselle Street, San Diego, CA 92121 (United States)

This paper describes a Python script that may be used to gather all required structure-annotation information into an mmCIF file for upload through the RCSB PDB ADIT structure-deposition interface. Almost all successful protein structure-determination projects in the public sector culminate in a structure deposition to the Protein Data Bank (PDB). In order to expedite the deposition proces, Deposit3D has been developed. This command-line script calculates or gathers all the required structure-deposition information and outputs this data into a mmCIF file for subsequent upload through the RCSB PDB ADIT interface. Deposit3D might be particularly useful for structural genomics pipeline projects because it allows workers involved with various stages of a structure-determination project to pool their different categories of annotation information before starting a deposition session.

• OSTI ID: 22356163
• Journal Information: Acta Crystallographica. Section F, Journal Name: Acta Crystallographica. Section F Journal Issue: Pt 9 Vol. 61; ISSN ACSFCL; ISSN 1744-3091
• Country of Publication: United Kingdom
• Language: English

Related Subjects

75 CONDENSED MATTER PHYSICS
SUPERCONDUCTIVITY AND SUPERFLUIDITY
DEPOSITION
INTERFACES
PROTEIN STRUCTURE
PROTEINS