mmcif in Structural Bioinformatics
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1 mmcif in Structural Bioinformatics John Westbrook Rutgers, The State University of New Jersey
2 Overview Brief history of mmcif development & implementation How the wwpdb archives structure, experimental, and reference data How mmcif is helping to address current challenges in data archiving Recent developments in wwpdb data deposition and delivery
3 PDBx/mmCIF Development Timeline IUCr mmcif Working Party IUCr mmcif Maintenance Group Core CIF V1 mmcif V1 Workshops mmcif V2 mmcif/core sync d York Tarrytown Brussels Rutgers St. Louis Seattle Glasgow Rutgers CARB Orlando EBI Honolulu DDL 1 DDL 2 mmcif +Extensions PDB Exchange Dictionary wwpdb One Archive One Dictionary Data mmcif wwpdb Common Deposition & Annotation System
4 PDB Exchange Dictionary Coordinate and supporting primary data Scientific Content Experimental descriptions for: X-ray/Neutron diffraction, NMR, Electron Microscopy, SAS & hybrid methods Protein production Molecular and chemical representation Biological and functional annotation Additional derivative data Functional assemblies, validation details, coordinate frame transformations, secondary & tertiary structural features, nucleic acid structural features,
5 PDB Exchange Dictionary Metadata Content Features of Data Items Definitions and examples Data types (primitives & regular expression patterns) Boundary values Controlled vocabularies Simple organization Tables and columns (categories) Related data item sets (subcategories) Chapters (category groups) Associations Referential integrity - parent-child relationships Interdependencies/exclusivity Methods
6 The Central Role of the Data Dic1onary Validation Tools PDB Exchange Dictionary PDBx/mmCIF XML Schema Deposi'on Tools RDF/OWL Harves'ng Tools PDBx Format Tools SQL Schema PDB mmcif XML RDF
7 Current Supported Archival Formats protein structure format universe PDB (ca. 1974) PDBx/mmCIF (ca. 1997) PDBML (ca. 2005) RDF (ca. 2011) PDB PDBx/ mmcif PDBML & RDF In managing the formats, PDBx is the master format.
8 PDB Format Example REMARK 3 DATA USED IN REFINEMENT.! REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57! REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.00! REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000! REMARK 3 COMPLETENESS FOR RANGE (%) : NULL! REMARK 3 NUMBER OF REFLECTIONS : 43316! REMARK 3! REMARK 3 FIT TO DATA USED IN REFINEMENT.! REMARK 3 CROSS-VALIDATION METHOD : NULL! REMARK 3 FREE R VALUE TEST SET SELECTION : NULL! REMARK 3 R VALUE (WORKING + TEST SET) : NULL! REMARK 3 R VALUE (WORKING SET) : 0.191! REMARK 3 FREE R VALUE Record- oriented : with fixed column format! REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL! REMARK 3 FREE R VALUE Metadata TEST SET COUNT in semi- structured : 2189 remarks! REMARK 3!! Documenta'on by example! Most widely used and supported archival format ATOM 1 N VAL A N ATOM 2 CA VAL A C ATOM 3 C VAL A C ATOM 4 O VAL A O ATOM 5 CB VAL A C
9 PDBx/mmCIF Format Example Name value pairs _exptl.entry_id 1XBB _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 Simple syntax Named data items Data seman'cs defined in the PDBx data dic'onary SoJware support in most popular languages Tables or loop_ s loop database_pdb_rev.num _database_pdb_rev.date _database_pdb_rev.date_original _database_pdb_rev.mod_type _database_pdb_rev.replaces _database_pdb_rev.status XBB? ? 1 1XBB? ? 1 1XBB?
10 PDBML Example <PDBx:entity_polyCategory> <PDBx:entity_poly entity_id="1"> <PDBx:type>polypeptide(L)</PDBx:type> <PDBx:nstd_linkage>no</PDBx:nstd_linkage> <PDBx:nstd_monomer>no</PDBx:nstd_monomer> <PDBx:pdbx_seq_one_letter_code> DIVLTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYYTTTLADG VPSRFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIK </PDBx:pdbx_seq_one_letter_code> <PDBx:pdbx_seq_one_letter_code_can> Three flavors of XML files: DIVLTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYYTTTLADG fully marked- up files VPSRFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIK files without atom records </PDBx:pdbx_seq_one_letter_code_can> files with a more space efficient encoding of atom </PDBx:entity_poly> records </PDBx:entity_polyCategory> Follows naming and seman'cs of the PDBx data dic'onary
11 RDF Example <?xml version="1.0" encoding="utf-8"?> <?xml-stylesheet type="text/xml" href=" <rdf:rdf xmlns:pdbo=" xmlns:rdfs=" xmlns:rdf=" <PDBo:PDBID rdf:about=" <rdfs:label>1gof</rdfs:label> </PDBo:PDBID> <rdf:description rdf:about=" <PDBo:entity.formula_weight> </PDBo:entity.formula_weight> Entry point for seman'c web and reasoning systems <PDBo:entity.id>1</PDBo:entity.id> <PDBo:entity.pdbx_description>GALACTOSE Translates data items OXIDASE</PDBo:entity.pdbx_description> in PDBx/mmCIF schema into triples <PDBo:entity.pdbx_ec> </PDBo:entity.pdbx_ec> <PDBo:entity.pdbx_number_of_molecules>1</PDBo:entity.pdbx_number_of_molecules> with URL iden'fiers <PDBo:entity.src_method>man</PDBo:entity.src_method> <PDBo:entity.type>polymer</PDBo:entity.type> Follows naming and seman'cs of the PDBx data dic'onary <PDBo:link_to_enzyme rdf:resource=" <PDBo:of_datablock hrp://pdbj.org/rdf/<pdbid>/<categoryname>/<pkey1>, rdf:resource=" <PDBo:referenced_by_entity_keywords rdf:resource=" <PDBo:referenced_by_entity_poly For example, hrp://pdbj.org/rdf/1gof/en'ty/1 rdf:resource=" <PDBo:referenced_by_entity_src_gen rdf:resource=" <PDBo:referenced_by_struct_asym rdf:resource=" <PDBo:referenced_by_struct_ref rdf:resource=" <rdf:type rdf:resource=" </rdf:description> </rdf:rdf>
12 Chemical Reference Data Chemical Component Dictionary Library of all polymer and non-polymer chemical components in PDB ~18,000 chemical component definitions 400 additional definitions of amino acid protonation variants ~700 new components released this year ~1700 component definitions updated this year Complimentary to the CCP4 monomer library
13 Chemical Reference Data Example loop chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_cartn_x _chem_comp_atom.model_cartn_y _chem_comp_atom.model_cartn_z _chem_comp_atom.pdbx_model_cartn_x_ideal _chem_comp_atom.pdbx_model_cartn_y_ideal _chem_comp_atom.pdbx_model_cartn_z_ideal _chem_comp_atom.pdbx_ordinal HYP N N N 0 1 N N N HYP CA CA C 0 1 N N S HYP C C C 0 1 N N N HYP O O O 0 1 N N N HYP CB CB C 0 1 N N N HYP CG CG C 0 1 N N R HYP CD CD C 0 1 N N N HYP OD1 OD O 0 1 N N N HYP OXT OXT O 0 1 N Y N HYP H H H 0 1 N Y N HYP HA HA H 0 1 N N N HYP HB2 1HB H 0 1 N N N HYP HB3 2HB H 0 1 N N N HYP HG HG H 0 1 N N N HYP HD22 1HD H 0 0 N N N HYP HD23 2HD H 0 0 N N N HYP HD1 HOD H 0 1 N N N HYP HXT HXT H 0 1 N N N # Atom names Stereochemistry & aromaticity Model coordinates Ideal coordinates
14 Biologically Interesting Reference Molecule Dictionary (BIRD) Contains ~630 chemical definitions for peptide inhibitors and antibiotics Unifies the representation of small polymers and single molecules with substantially polymeric chemical structure Provides structural and functional annotations Designed to facilitate both sequence and detailed chemical structure searches Target Hit
15 Keeping Pace with Structural Biology The most enduring and widely used archival PDB format is not keeping pace with new science and technology. Efforts to work around PDB format limitations are increasingly problematic. PDB mmcif PDBx Reversible translation no longer practical. mmcif / PDBx
16 Challenges of Molecular Size PDB column format limitations 1-character for polymer chain labels 5-characters for atom serial numbers 3-characters for monomers and ligand identifiers 5-characters for atom names F8.3 for model coordinates Implications Maximum of 62 chains (upper and lower case!) Maximum of 99,999 atoms Requires splitting structures across multiple entries (5 ribosomes in ASU stored in 10 PDB entries!) Map and experimental validation are difficult for split entries Cannot use standard monomer & ligand nomenclatures (e.g. carbohydrates & protonation variants) Cannot use conventional atom names in large ligands Limits molecular dimension (< Angstroms) 1VOQ
17 Representing Evolving Content PDB Record format limitations The small number of named records are not extensible (e.g. ATOM, CONECT, SEQRES, ). Text REMARKS with ad hoc formats hold all other meta-data. Implications No bond orders are specified for ligands ATOM records tailored for traditional X-ray methods and inflexible for newer methods (e.g. TLS groups) Sequence and coordinate residue correspondence is ambiguous and there is no support for heterogeneity. Growing diversity and complexity of REMARK records has become unmanageable for both deposition and archiving No standard and extensible way to represent and document meta-data
18 Key Format Goals for PDB Represent all PDB model structure, supporting experimental and metadata Provide a working format for data exchange between the laboratory and the archive Support the entire structure biology pipeline: modelbuilding, refinement, visualization, validation, analysis, simulation, prediction, New Format in the Lab wwpdb Annotation Deposition Phenix Amber Rosetta PDBx/ mmcif Chimera RDF Current PDB Format Round Trip New Format PDBML
19 Finding a Simple Format Alternative 2010 started process of defining new format, consulting many software developers 2011 Developers Workshop - agreement to adopt PDBx (mmcif) as the new format and to phase out the old PDB format Commitments from CCP4, Phenix and Global Phasing (i.e., ~85% of all PDB depositions) Agreement on managing development between these software providers and wwpdb Established PDBx Deposition Working Group Working Group recommendations and implementations in CCP4 and Phenix.
20 PDBx/mmCIF Deposition Working Group PDBx Deposition Working Group Refinement Developers Workshop EBI In 2011, charged with finding a round trip single format that can handle complex data not supported by the PDB file format Consensus reached on using dictionary-driven PDBx format Implementations delivered in January 2013 PDBx Format in the Lab Structure Determination Pipeline wwpdb Deposition wwpdb Processing and Annotation Round Trip PDBx Format in wwpdb ftp Archive
21 Working Group Recommendations Announced 22-May-2013 Format extensions for large structures: Atom serial numbers (1 to the number atoms) Chain identifiers up to 4 characters Cartesian coordinates with field widths as required and 3 decimal places B-factors and occupancies with 3 decimal places precision. Implement extensions as required to as maintain backward compatibility
22 Transitional Home for Large Structures Large single entries are now stored separately on the wwpdb ftp site, and PDB internally produces divided/split PDB format files. ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmcif/ ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/xml/ HIV-1 Capsid 3J3Q 1356 chains >2M atoms 25 PDB format entries 3J3Y 3J3Q
23 Providing Format Compatibility Adopt a PDB friendly mmcif/pdbx style - All records on a single text line Columns presented in standard column order. Tabular presentation with leading record names (e.g. ATOM, CELL, REFINE) Method independent features in left-most columns (e.g. identifiers & coordinates) Method specific features in the right-most columns (e.g. ADPs, NMR order/disorder parameters) Continue to support PDB nomenclature semantics (e.g. PDB style chains, residue numbering, and insertion codes) Large entries will be internally converted to divided/split PDB format files.
24 ATOM 1 N GLN A N ATOM 2 CA GLN A C ATOM 3 C GLN A C ATOM 4 O GLN A O ATOM 5 CB GLN A C ATOM 6 N VAL A N ATOM 7 CA VAL A C ATOM 8 C VAL A C ATOM 9 O VAL A O ATOM 10 CB VAL A C PDB loop atom_site.group_pdb _atom_site.id _atom_site.auth_atom_id _atom_site.type_symbol _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_seq_id _atom_site.cartn_x _atom_site.cartn_y _atom_site.cartn_z _atom_site.pdbx_pdb_model_num _atom_site.occupancy _atom_site.pdbx_auth_alt_id _atom_site.b_iso_or_equiv ATOM 1 N N GLN A ATOM 2 CA C GLN A ATOM 3 C C GLN A ATOM 4 O O GLN A ATOM 5 CB C GLN A ATOM 6 N N VAL A ATOM 7 CA C VAL A ATOM 8 C C VAL A ATOM 9 O O VAL A ATOM 10 CB C VAL A ATOM 11 N N ALA A PDBx/mmCIF
25 New wwpdb Deposition & Annotation System mmcif/pdbx End-to-end support for PDBx/mmCIF
26 PDBx/mmCIF Software Support Phenix and Refmac produce native PDBx files for deposition MMDB - macromolecular object library in CCP4 iotbx.cif/ucif - CCTBx C++/Python IO library with dictionary validation CCIF CCP4 C++ library with FORTRAN support and dictionary validation CBFLib - ANSI-C library for CIF & imgcif files mmlib - Python toolkit supporting CIF & mmcif BioPython - Python toolkit for computational biology PyCifRW - Python CIF/mmCIF parsing tools BioJava - Java mmcif IO package STAR::Parser Perl mmcif parser and molecular object library RCSBTools - C++/Python parsing and dictionary validation tools plus many other supporting format conversion and data management applications Visualization - Chimera, Jmol, OpenRasMol PDB actively working with community developers to help fill in missing functionalities. Two workshops scheduled in Fall 2013
27 NSF, NIGMS, DOE, NLM, NCI, NINDS, NIDDK NLM EMBL- EBI, Wellcome Trust, BBSRC, NIGMS, EU NBDC- JST wwpdb
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