Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB

• Published in: Structure (London) Vol. 21; no. 6; pp. 875 - 881
• Main Authors: Trewhella, Jill, Hendrickson, Wayne A., Kleywegt, Gerard J., Sali, Andrej, Sato, Mamoru, Schwede, Torsten, Svergun, Dmitri I., Tainer, John A., Westbrook, John, Berman, Helen M.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 04-06-2013
• Subjects: Archives; Archiving; Biology; Databases, Protein; Models, Molecular; Protein Conformation; Proteins - chemistry; Repositories; SAS; Scattering; Scattering, Small Angle; Tasks
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2013.04.020

This report presents the conclusions of the July 12–13, 2012 meeting of the Small-Angle Scattering Task Force of the worldwide Protein Data Bank (wwPDB; Berman et al., 2003) at Rutgers University in New Brunswick, New Jersey. The task force includes experts in small-angle scattering (SAS), crystallography, data archiving, and molecular modeling who met to consider questions regarding the contributions of SAS to modern structural biology. Recognizing there is a rapidly growing community of structural biology researchers acquiring and interpreting SAS data in terms of increasingly sophisticated molecular models, the task force recommends that (1) a global repository is needed that holds standard format X-ray and neutron SAS data that is searchable and freely accessible for download; (2) a standard dictionary is required for definitions of terms for data collection and for managing the SAS data repository; (3) options should be provided for including in the repository SAS-derived shape and atomistic models based on rigid-body refinement against SAS data along with specific information regarding the uniqueness and uncertainty of the model, and the protocol used to obtain it; (4) criteria need to be agreed upon for assessment of the quality of deposited SAS data and the accuracy of SAS-derived models, and the extent to which a given model fits the SAS data; (5) with the increasing diversity of structural biology data and models being generated, archiving options for models derived from diverse data will be required; and (6) thought leaders from the various structural biology disciplines should jointly define what to archive in the PDB and what complementary archives might be needed, taking into account both scientific needs and funding.