1. Enabling Rapid Interaction with the Protein Data Bank
Alexy Khrabrov
Rutgers University
John D. Westbrook

2. Goals
Provide application and database access to macromolecular structure data
Follow standards-based approach (OMG MMS finalized 2001)
Build on informatics structure of PDB data ontology
Provides high performance access
Direct access to compact binary data structures (e.g. coordinates)
Provide broad granularity of access (individual atoms to biological assemblies)

3. Program Level Access to the Details of Molecular Structure
Ligand – Which ligands are contained within the entry?
Chain/Entity – Extract the sequence and coordinates for each molecular entity.
Secondary Structure – Extract helices and sheets for the entry.
Residues/Atoms - What is the
environment of this residue? Extract the coordinates for a selection of atoms or residues.

4. API Architecture Features
API organization based on PDB Exchange Data Dictionary - access methods are provided at the level of data categories/classes
PDB Exchange Dictionary provides the content to automatically generate:
OMG Interface Definition Language (IDL) and access classes
SQL queries required to support Corba server
Software to load PDB datafiles in memory or into a supporting relational database engine

5. Current Data Dictionaries http://deposit.pdb.org/mmcif/
PDB data exchange (XML Schema/CIF)
Including structural genomics and data harvesting extensions
mmCIF
NMR
3D-EM
Modeling
Crystallization
Symmetry
Image data
BIOSYNC 27

6. Extending Data Dictionaries for Deposition
X-ray
macromolecular naming, source organism, crystallization and cell parameters, data collection, structure solution and phasing, model building, refinement, model quality
NMR
explicit details on sample preparation, contents and conditions, constraints, force constants, related statistics
Protein Production
source information, target gene production, bacterial cloning, bacterial expression, purification 29

7. Elements of Dictionary Metadata
Data Attributes
Definition
Examples
Data type (primitive type/regular expression patterns)
Range or allowed values
Classes
Categories
Subcategories
Category groups
Associations
Parent-child relationships
Interdependencies/exclusivity
Methods

8. Automatic Production of Macromolecular Structure API Components
Metamodel
Framework
PDB Exchange Dictionary + API Specific Data Dictionaries
CORBA IDL, SQL Schema,
XML DTD/Schemas,
Data Loaders
Database Access Classes

9. Macromolecular Structure API Data Flow
mmCIF
Parsers
Applications
XML Files
mmCIF Data Files
(Data Reference Standard)
Relational
Database
CORBA
Server

10. Metadata Framework PDB Exchange Dictionary Grouping Dictionary
Defines content model
Grouping Dictionary
Maps dictionary content to API organization
Assigns attributes to API aggregate data types and indices
Schema Mapping Dictionary
Maps content to physical storage layer 29

11. Automatic Generation of IDL
Metadata framework is input data for automated generation of Corba IDL
IDL is a platform independent definition of API
IDL is used to produce client stubs and server skeleton classes on any platform 29

12. Automatic Generation of API Server
Metadata framework is input data for automated generation of server access classes -
SQL access methods
Implementation of abstract skeleton methods using DB2 CLI
Integrate with any custom server methods 29

13. API Server Extension
Extend content model through PDB exchange data dictionary
Extend supporting dictionaries in metadata framework
Autogenerate IDL
Autogenerate skeleton implementations
Integrate custom code 29

14. Supporting Alternative APIs
Adapt IDL autogenerator
Revise MDF->IDL to MDF->new API spec
Adapt autogenerator of server skeleton implementations
Integrate custom methods 29

15. Server Availability
OpenMSS toolkit provides Java interface to Oracle/MySQL using JDBC (core mmCIF classes)
C++ server using native interface to DB2 (EEE) implemented on 4-node Linux cluster (NDB beta test in Sept.)
Installation of DB2 (EEE) at SDSC underway to support high-performance access 29

16. Client Program Examples
DsMmsMacromolecularStructure.idl excerpt:
struct AtomSite {
string id;
IndexId type_symbol;
AtomIndex label;
IndexId label_entity;
VectorXYZ cartn;
float occupancy;
float b_iso_or_equiv; };

17. Client Program Examples
A primary requirement of the design was that it present an interface that was clearly defined and easy to use from the point of view of developing new applications. The code examples in this section illustrate how client programs can use the API to quickly access macromolecular structure data. As a simple example the following Python code fragment will print out the atom identifier and the Cartesian (x, y, z) position for atoms in the macromolecule 4hhb.
Example 1. Retrieving the AtomSite list for hemoglobin (4HHB) and printing the atomic coordinates.
try:
sid = ”4HHB"
e = ef.get_entry_from_id(sid);
except:
print "cannot get entry %s, exiting!" % sid
sys.exit(1)
print "got entry!"
# Get the atom site list
atoms = e.get_atom_site_list()
print "got %d atoms total" % (len(atoms))
print "A few atoms:"
for a in atoms[:10]:
print "%s\t%.3f %.3f %.3f" %
(a.id, a.cartn.x, a.cartn.y, a.cartn.z)

18. # Get the symmetry information s = e.get_sym_info()
Example 2. Listing symmetry information and the residues ranges for the helices of the hemoglobin (4HHB).
# Get the symmetry information
s = e.get_sym_info()
print "space group: %s" % s.space_group
print "cell constants: "
c = s.acell.unit_cell
print "a=%.3f, b=%.3f, c=%.3f" % \
(c.length_a, c.length_b, c.length_c)
print "alpha=%.3f, beta=%.3f, gamma=%.3f" % \
(c.angle_alpha, c.angle_beta, c.angle_gamma)
# Get the secondary structures
sconfs = e.get_struct_conf_list()
print "Secondary structures:"
for a in sconfs:
print a.id, '\t', \
a.beg_auth.asym.id, a.beg_auth.comp.id, a.beg_auth.seq.id, \
'\t-->', \
a.end_auth.asym.id, a.end_auth.comp.id, a.end_auth.seq.id

19. Client Availability
Example clients provide category-level access in Java OpenMMS and C++ native servers
Clients available in Java, C++ and Python
C++ API extended to support efficient detailed molecular selections (e.g. coordinates of secondary structure elements, symmetry related molecular elements, biological assemblies) 29

20. Access Protein Data Bank Site OpenMMS site (Java implementation)
OpenMMS site (Java implementation)
PDB Software Download Site (C++ and Python implementation)
/mmcif/FILM/
PDB Dictionary Resource Site
/mmcif/
PDB Beta Data Site
ftp://beta.rcsb.org/pub/pdb/uniformity/data/ 29