Data File Formats. There are dozens of file formats for chemical data.
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1 1 Introduction There are dozens of file formats for chemical data. We will do an overview of a few that are often used in structural bioinformatics. 2 1
2 PDB File Format (1) The PDB file format specification is rather extensive. A tutorial on the topic can be found at: A PDB file includes the following information: HEADER First line of the file, contains PDB ID code, classification, and date of deposition. COMPND A description of the macromolecular contents. SOURCE Biological source of the macromolecule. REVDAT Revision dates. JRNL Reference to journal article dealing with this structure. 3 PDB File Format (2) A PDB file information continued: AUTHOR List of contributors. REMARK General remarks, some structured, some free form. SEQRES Primary sequence of the residues on a protein backbone. SEQRES 1 A 99 PRO GLN ILE THR LEU TRP GLN ARG PRO LEU VAL THR ILE 1HVS 91 SEQRES 2 A 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR 1HVS Serial Number 12 Chain ID 20+4*n 22+4*n n=0,1,2,, 12 Residue Names Number of Residues Integers in red boxes are column numbers PDB ID File Line Number 4 2
3 PDB File Format (3) For your assignment the most important type of record is that ATOM record: Contains the coordinates of a particular atom Serial Number Residue Name Residue Seq num Occupancy PDB ID File Line Number ATOM 1 N PRO A HVS 136 ATOM 2 CA PRO A HVS 137 ATOM 3 C PRO A HVS Atom Name 22 Chain ID X, Y, Z Coordinates in Angstroms Temperature Factor The list of ATOM records in a chain is terminated by a TER record. 5 PDB File Format (4) Other record types: HET Names of hetero-atoms Usually designates atoms and molecules that are separate from the protein. FORMUL Chemical formula for the hetero-atoms. HELIX Location of helices (designated by depositor). SHEET Location of beta sheets (designated by depositor). SSBOND Location of disulfide bonds (if they exist). ORIGn Scaling factors to transform from orthogonal coordinates. SCALEn Scaling factors transforming to fractional crystal coordinates. 6 3
4 A New File Format: mmcif Macromolecular Crystallographic Information File Derived from CIF S.R. Hall, F.H. Allen, and I.D. Brown The Crystallographic Information File (CIF): a new standard archive file for crystallography. Acta Cryst. (1991). A47, Dictionary based The macromolecular CIF dictionary is a set of data names designed to describe the macromolecular crystallographic experiment and its results. Each data item in a mmcif matches an entry in the dictionary. This enables the validation of data and gives a more consistent representation of structures. Easier to parse with less ambiguity. 7 Comparing PDB Files and mmcif (1) PDB Header: HEADER HYDROLASE(ACID PROTEASE) 26-JAN-94 1HVI becomes: _struct.entry_id 1HVI _struct.title ;INFLUENCE OF STEREOCHEMISTRY ON ACTIVITY AND BINDING MODES FOR C2 SYMMETRY-BASED DIOL INHIBITORS OF HIV-1 PROTEASE ; _struct_keywords.entry_id 1HVI _struct_keywords.pdbx_keywords 'HYDROLASE(ACID PROTEASE)' _struct_keywords.text 'HYDROLASE(ACID PROTEASE)' 8 4
5 Comparing PDB and mmcif (2) The equivalent of ATOM records: loop atom_site.group_pdb _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_pdb_ins_code _atom_site.cartn_x _atom_site.cartn_y _atom_site.cartn_z _atom_site.occupancy _atom_site.b_iso_or_equiv _atom_site.cartn_x_esd _atom_site.cartn_y_esd _atom_site.cartn_z_esd _atom_site.occupancy_esd _atom_site.b_iso_or_equiv_esd _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_pdb_model_num 9 Comparing PDB and mmcif (3) The equivalent of ATOM records (cont.): ATOM 1 N N. PRO A 1 1? ????? 1 PRO A N 1 ATOM 2 C CA. PRO A 1 1? ????? 1 PRO A CA 1 ATOM 4 O O. PRO A 1 1? ????? 1 PRO A O 1 PDB records for these first three atoms: ATOM 1 N PRO A ATOM 2 CA PRO A ATOM 3 C PRO A
6 Comparing PDB and mmcif (4) To see a good tutorial on mmcif you can visit the SDSC (San Diego Supercomputer Center): This includes many examples of how dictionary entries and their associated values appear in a typical mmcif file. There are also several interesting links from their homepage. 11 PubChem File Formats: ASN.1 (1) ASN.1 (Abstract Syntax Notation 1): A standardized data specification language used to represent complex data types. Data structure is hierarchical Designed by Xerox A formal notation used for describing data transmitted by telecommunications protocols and physical representation of such data. Also used in telephone systems, air traffic, building and machine control, toll highways, smart cards, security and much more. Used by NCBI to store GenBank, PubMed, MMDB. National Center for Biotechnology Information 12 6
7 PubChem File Formats: ASN.1 (2) Abstract Syntax Notation 1 for water: ETC. 13 PubChem File Formats: XML (1) Extensible Markup Language Is a general-purpose markup language that supports a wide variety of applications. Just like HTML it is also built around an hierarchical layout that uses markup tags. It is quite versatile. Almost human readable. However, files tend to be rather long. The PubChem entry for water has an XML file that is 406 lines long! The first few lines of this file appear next: 14 7
8 PubChem File Formats: XML (2) Water in XML: 15 PubChem File Formats: XML (3) Water in XML (cont.): lines to go 8
9 PubChem File Formats: SDF (1) SDF is a chemical file format File extensions:.mol.sd.sdf A MDL Molfile is a file format designed by MDL, for storing data about the atoms, bonds, connectivity and atom coordinates of a molecule. The molfile consists of header information, the Connection Table (CT) containing atom information, bond connections and types, followed by records for more complex information. The format is owned by MDL (Molecular Design Limited). 17 PubChem File Formats: SDF (2) SDF for glycine (CID 750): 18 9
10 PubChem File Formats: SDF (3) SDF for glycine (CID 750) Other useful information: <PUBCHEM_CACTVS_HBOND_ACCEPTOR> 3 > <PUBCHEM_CACTVS_HBOND_DONOR> 2 > <PUBCHEM_CACTVS_ROTATABLE_BOND> 1 > <PUBCHEM_IUPAC_NAME> 2-aminoacetic acid > <PUBCHEM_NIST_INCHI> InChI=1/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)/f/h4H > <PUBCHEM_CACTVS_XLOGP> -3.4 > <PUBCHEM_OPENEYE_MF> C2H5NO2 > <PUBCHEM_OPENEYE_MW> > <PUBCHEM_OPENEYE_CAN_SMILES> C(C(=O)O)N 19 10
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