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Enabling Rapid Interaction with the Protein Data Bank. Alexy Khrabrov Rutgers University John D. Westbrook Rutgers University. Goals. Provide application and database access to macromolecular structure data Follow standards-based approach (OMG MMS finalized 2001)

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enabling rapid interaction with the protein data bank

Enabling Rapid Interaction with the Protein Data Bank

Alexy Khrabrov

Rutgers University

John D. Westbrook

Rutgers University

  • 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)
program level access to the details of molecular structure
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.

api architecture features
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
current data dictionaries http deposit pdb org mmcif
Current Data Dictionarieshttp://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
extending data dictionaries for deposition
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
elements of dictionary metadata
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
automatic production of macromolecular structure api components
Automatic Production of Macromolecular Structure API Components



PDB Exchange Dictionary + API Specific Data Dictionaries


XML DTD/Schemas,

Data Loaders

Database Access Classes

macromolecular structure api data flow
Macromolecular Structure API Data Flow




XML Files

mmCIF Data Files

(Data Reference Standard)





metadata framework
Metadata Framework
  • PDB Exchange 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
automatic generation of idl
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
automatic generation of api server
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
api server extension
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
supporting alternative apis
Supporting Alternative APIs
  • Adapt IDL autogenerator
    • Revise MDF->IDL to MDF->new API spec
  • Adapt autogenerator of server skeleton implementations
  • Integrate custom methods
server availability
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
client program examples
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;


client program examples1
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.


sid = ”4HHB"

e = ef.get_entry_from_id(sid);


print "cannot get entry %s, exiting!" % sid


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)

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

client availability
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)
  • Protein Data Bank Site
    • http://www.pdb.org/
  • OpenMMS site (Java implementation)
    • http://openmms.sdsc.edu
  • PDB Software Download Site (C++ and Python implementation)
    • http://deposit.pdb.org /mmcif/FILM/
  • PDB Dictionary Resource Site
    • http://deposit.pdb.org /mmcif/
  • PDB Beta Data Site
    • ftp://beta.rcsb.org/pub/pdb/uniformity/data/