Conference Agenda

Overview and details of the sessions of this conference. Please select a date or location to show only sessions at that day or location. Please select a single session for detailed view (with abstracts and downloads if available).

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Session Overview
Session
SMS-2: Exemplary practice in chemical, biological and materials database archiving
Time:
Monday, 16/Aug/2021:
2:45pm - 5:10pm

Session Chair: Suzanna Ward
Session Chair: Genji Kurisu
Location: 221-2

60 2nd floor

Invited: Ian Bruno (UK), Stephen Burley (USA)


Session Abstract

Crystallographic databases have a long and distinguished history. The Cambridge Structural Database (CSD) has been in operation for more than 50 years and is reaching its millionth published crystal structure entry. The Protein Data Bank was founded in 1971 and has around 150,000 entries, mainly derived from X-ray crystallography but also from NMR, cryoEM and neutron crystallography and integrative methods. The validation of entries is a major effort, and one that could act as an exemplar for other scientific fields. The science educational use of the entries is absolutely gargantuan. The impact on science and medicine based industries is huge. The microsymposium will explore best practice in archiving and the development of tools for optimal dissemination of the data curated by the database organisations. The modern challenge for databases also includes handling of results from scattering, diffraction, spectroscopies and microscopies, once again from the full spectrum of samples such as crystals, powders, fibres, nanostructured and amorphous materials or solutions. Also in recognition of the growing interest and indeed importance given to raw data, both the CSD and PDB now invite the author/depositor to include DOIs registered for raw diffraction data images and associated metadata.

 


Introduction
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Presentations
2:45pm - 2:50pm

Introduction to session

Suzanna Ward, Genji Kurisu



2:50pm - 3:20pm

CSD One Million: Reasons why the crystallographic community is exemplary

Ian Bruno, Natalie Johnson, Matthew Lightfoot, Suzanna Ward

The Cambridge Crystallographic Data Centre, Cambridge, United Kingdom

The recent surpassing of 1 million structures in the Cambridge Structural Database [1] offered a moment for celebration and an opportunity to reflect. Achieving this significant milestone is a testament to the exemplary initiatives and engagement emanating from the crystallographic community over many decades. The development of semantic representation formats [2], the cultivation of joined-up publishing workflows, and the broad adoption of standards all pre-empted the principles, guidelines and practices that have come to dominate the discourse around research data preservation and reuse today [3]. We cannot however rest on our laurels. The curation activities of organisations such as the Cambridge Crystallographic Data Centre remain of critical importance and must continue to evolve. We must ensure that our data resources remain relevant and can be readily utilised by the data-driven approaches being applied to the complex scientific problems of today.

This presentation will offer reflections on the successes of the crystallographic community that have been critical in ensuring the outputs of the past can conform to the expectations and demands of the future. It will highlight how these have enabled a wealth of structural chemistry knowledge to be applied across industry and academia to innovate and educate [4]. Additionally, it will look at the challenges and opportunities presented by an evolving research publication landscape, new experimental and computational methods, and the desire for greater reproducibility and richer reuse of structural chemistry data.

[1] Groom C. R., Bruno I. J., Lightfoot M. P. & Ward S. C. (2016). Acta Crystallogr. Sect. B Struct. Sci. Cryst. Eng. Mater. 72(2), 171.

[2] Hall S. R. & McMahon B. (2016). Data Sci. J. 15(3), 1.

[3] Wilkinson M. D., Dumontier M., Aalbersberg IjJ., et al. (2016). Sci Data. 3(1), 1.

[4] Taylor R., Wood P. A. (2019) Chem Rev. 119(16), 9427.

External Resource:
Video Link


3:20pm - 3:50pm

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

Stephen K. Burley

Rutgers, The State University of New Jersey, Piscataway, United States of America

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including > 800 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators, and students studying fundamental biology, biomedicine, biotechnology, bioengineering, and energy sciences. During the past two years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with > 40 external biodata resources. New features and resources will be described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.

External Resource:
Video Link


3:50pm - 4:15pm

Behind the scenes - data processing and quality assurance for the ICSD

Annett Steudel, Stephan Rühl

FIZ Karlsruhe - Leibniz-Institut für Informationsinfrastruktur, Eggenstein-Leopoldshafen, Germany

The Inorganic Crystal Structure Database (ICSD) has been collecting published crystal structures for more than 40 years. In addition, the database offers the structures in curated and extended form. In the process of adding a structure to the database, a series of tests are run to verify data integrity and correctness. Furthermore, the data is enriched with additional or missing information, which can help to detect possible discrepancies. Some of the procedures used will be explained here, and examples will be given to show how careful evaluation of crystallographic parameters and the addition of missing parameters improves the quality of the crystal structure entry.

External Resource:
Video Link


4:15pm - 4:40pm

The Full Plate: Benefits of simulated and raw data digital patterns in the Powder Diffraction FileTM

Stacy Gates-Rector, Thomas Blanton, Vesna Bosnic, Soorya Kabekkodu, Justin Blanton

International Centre for Diffraction Data, Newtown Square, United States of America

The Powder Diffraction File™ (PDF®) is a comprehensive materials database containing data for inorganic materials including minerals (natural and synthetic), metals and alloys, and high-tech ceramics, as well as organic materials such as pharmaceuticals, excipients and polymers. Databases, including the PDF, that provide structural details can be used for a range of materials characterization analyses, including (but not limited to) phase identification, quantitative analysis, and structure modelling for Rietveld refinement and whole-pattern fitting. As a result, structural databases are one of the key tools used in the crystallographic community [1]. Though these databases do tend to have some common applications, they often differ in content, format, and functionality. ICDD’s PDF databases primary purpose is to serve as a quality reference tool for the powder diffraction community.

Historically, the PDF has contained entries constructed as d-spacing and intensity (d-I) reduced diffraction pattern representations for phase identification. These condensed entries reduced storage space requirements, and increased search speed capabilities. With the advancement of computer hardware and software, and the transition of the PDF to a relational database format, storage space and speed capabilities have become less limiting [2]. Over time the PDF has grown exponentially, and has evolved to where it is now common practice to construct entries of full digital patterns. In addition to being a powerful characterization database used for the analysis of single and multi-phase X-ray diffraction data, the ICDD has systematically been adding raw data digital pattern references for crystalline and non-crystalline materials since 2008; with an emphasis on excipients and polymers [3]. The addition of full digital patterns has enabled the analysis and identification of disordered and amorphous materials using a combination of the raw data pattern and d-I lists, or whole pattern similarity searching. The evolution of raw data archiving in the Powder Diffraction File will be discussed in this presentation, with emphasis on the benefits and increased capabilities for characterization of materials in both research and industrial applications including pharmaceutical, forensic, and energy sectors.

[1] Kuzel, R. and Danis, S. (2007). Mater. Struct. Chem., Biol., Phys. Technol. 14, pp.89–96.

[2] Gates-Rector, S., & Blanton, T. (2019). Powder Diffraction, 34(4), pp. 352-360.

[3] Fawcett, T., Gates-Rector, S., Gindhart, A., Rost, M., Kabekkodu, S., Blanton, J., & Blanton, T. (2019). Powder Diffraction, 34(2), pp. 164-183.

External Resource:
Video Link


4:40pm - 5:05pm

Protein Data Bank Japan: 20 years and more as the Asian hub for 3D structure and the founding member of the wwPDB

Genji Kurisu

Osaka University, Osaka, Japan

Protein Data Bank Japan (PDBj) accepts and processes regional 3D structure data of biological macromolecules since 2000. We celebrated our 20th anniversary of our regional Data-in activities last year. Our Data-out service has a much longer history, dating back to before the establishment of PDBj. The first protein structure from Asia was determined at the Institute for Protein Research (IPR) in 1971 at 4 Å [1] and a subsequent structure at 2.3 Å solved in 1973 [2] was deposited to the PDB in 1975 as the 21st entry in PDB. Based on these early contributions to the crystallographic community, IPR founded the Crystallographic Research Centre and installed several 4-circule diffractometers, and developed the Imaging Plate detectors of R-axis series later [3] together with Rigaku. In addition to above activities, IPR was assigned as the National Affiliated Centre of Cambridge Crystallographic Data Centre from 1978 and keep serving until now (http://www.protein.osaka-u.ac.jp/CSD/, Fig.1). Distribution of the PDB data from IPR started in 1979 as a regional data centre, initially by magnetic tape and later by CD-ROM, until the installation of an official mirror site of Brookhaven PDB in 1998. Since 2001, we have provided our newly developed online Data-out services freely and publicly through our own web site (https://pdbj.org; Fig.2), which includes our molecular graphics viewer, Molmil; a molecular surface database for functional sites, eF-site; and a database of protein dynamics calculated via normal mode analysis, Promode Elastic [4], and we have served since 2003 as a founding member of the worldwide PDB (https://wwpdb.org). During the COVID-19 pandemic, we have provided a COVID-19 featured page in three Asian languages (Japanese, Chinese and Korean) and have started a new service archiving raw X-ray image data directly related to deposited PDB entries (XRDa, https://xrda.pdbj.org; Fig.3) [5]. Since we already have BMRBj (formerly PDBj-BMRB) and EMPIAR-PDBj on-site, XRDa completes the regional experimental raw data archives of the related PDB, BMRB and EMDB entries from the three major experimental methods; Macromolecular Crystallography, NMR spectroscopy and 3D Electron Microscopy.

[1] Ashida, T., Ueki, T., Tsukihara, T., Sugihara, A., Takano, T. & Kakudo, M. (1971) J. Biochem. 70, 913–924. [2] Ashida, T., Tanaka, N., Yamane, T., Tsukihara, T. & Kakudo, M. (1973) J. Biochem., 73, 463–465.

[3] Sato, M., Katsube, Y. & Hayashi, K. (1993) J. Appl. Cryst., 26, 733-735.

[4] Kinjo, A.R., Bekker, G.-J., Wako, H., Endo, S., Tsuchiya, Y., Sato, H., Nishi, H., Kinoshita, K., Suzuki, H., Kawabata, T., Yokochi, M., Iwata, T., Kobayashi, N., Fujiwara, T., Kurisu, G. & Nakamura, H. (2018) Protein Sci., 27, 95-102.

[5] Bekker, G.-J. & Kurisu, G. in preparation

External Resource:
Video Link


 
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