Annual Scientific Report 2015

Sameer Velankar
PDBe Content and Integration
PhD, Indian Institute of Science, 1997.
Postdoctoral researcher, Oxford University,
United Kingdom, 1997-2000.
wwPDB validation pipeline, users can now identify “best
quality” structures for given macromolecules based on
our newly designed data-access mechanisms.
We implemented new data query systems and web
pages in a user-centric approach, with user surveys and
input at critical stages of the development. We initiated
user involvement with a survey to establish essential
requirements. The results of the survey and feedback on
early prototypes informed the design of the new query
system and web pages. We then developed new ways of
presenting structure data to help non-expert biologists
understand the structure information. A set of images
providing rich insights into the quaternary structure
or ligand-binding sites, or displaying sequence and
structure domain annotations, now helps users with
different levels of expertise understand the structure
data available in the PDB. We integrated interactive
web components showing annotations on sequence
(1D) and structure (3D) data on the new entry pages.
When user feedback suggested that general biologists
struggled with these displays, we implemented an
interactive topology (2D) viewer to provide a more
seamless link between sequence-based data and 3D
structure. The viewer displays such information on the
topology diagram, which provides a schematic view of
the arrangement of secondary structure elements in
the tertiary structure. These diagrams are a result of a
collaboration between PDBe and Dr Roman Laskowski
from the Thornton research group.
The new query system provides an easy-to-use interface
and basic data-analysis capabilities. It allows users
to browse structure entries in the archive and offers
filters for “drilling down” to a subset of entries. It also
allows users to identify the most suitable structure
from a given set by grouping entries based on unique
macromolecules, small molecules and sequence
families, displaying the “best” quality structure based on
wwPDB validation data.
Our new search system offers extended functionality
developed in the BioSolr project, a close collaboration
between PDBe, the Samples, Phenotypes and Ontologies
team and Flax, a Cambridge-based search technology
company. A new plugin developed by BioSolr to integrate
external programs now enables users to query PDB
entries based on sequence. Following usability testing,
the new feature will be released in 2016.
The team also publicly released a REST API to provide
both query access and entry information for PDB and
EMDB entries. The widely used 3D structure viewer
Jmol/JSmol and the interactive sequence-analysis
application JalView both make use of the API. It is used
internally to ensure data consistency across all PDBe
services, and provides access to value-added annotation
from the SIFTS resource and data-quality information
from the wwPDB validation data.
At EMBL-EBI since 2000.
Team leader since 2011.
The wwPDB now uses the infrastructure
developed in 2014 to integrate small-molecule crystal
structures from the Cambridge Structural Database
(CSD) into the PDB Chemical Component Dictionary
(CCD). In 2015, a file containing information on 1418
chemical components found to be common between the
CCD and CSD was released in the wwPDB public ftp
area.
Future plans
We will continue to work on the wwPDB common
deposition and annotation system to extend its
functionality to include more experimental techniques.
A major update, version 2.0, will be implemented at all
wwPDB sites in 2016. This will allow PDBe to process
all European and African depositions for both PDB and
EMDB. We plan to continue improving the data quality
of PDB and EMDB archive entries. We will also adapt
PDBe services that provide value-added annotations and
data analysis so that they can be integrated into the new
infrastructure. We will implement major improvements
to the PDBe query interface and entry pages, responding
to user needs in terms of functionality and data access.
As additional value-added information becomes
available, we will extend the PDBe REST API so that the
information can be accessed programmatically. To make
our users aware of new developments, we will continue
to participate in and organise international conferences,
workshops and training events, engage on social media
and publish scholarly articles.
Selected publications
Gutmanas A, et al. (2015) NMR Exchange Format: a
unified and open standard for representation of NMR
restraint data. Nat. Struct. Mol. Biol. 22:433-434
Lewis TE, et al. (2015) Genome3D: exploiting structure
to help users understand their sequences. Nucleic Acids
Res. 43:D382-D386
Meldal BH, et al. (2015) The complex portal--an
encyclopaedia of macromolecular complexes. Nucleic
Acids Res. 43:D479-D484
Sali A, et al. (2015) Outcome of the First wwPDB hybrid/
integrative methods task force workshop. Structure
23:1156-1167
Westbrook JD, et al. (2015) The chemical component
dictionary: complete descriptions of constituent
molecules in experimentally determined 3D
macromolecules in the Protein Data Bank.
Bioinformatics 31:1274-1278
2015 EMBL-EBI Annual Scientific Report 110