PDB file format

An alternative and much more flexible approach is represented hy the STAR file format [L48, 149, which can be used for building self-describing data files. Additionally, special dictionaries can be constructed, which specify more precisely the contents of the eorresponding data files. The two most widely used such dictionaries (and file formats) arc the CIF (Crystallographic Information File) file format [150] - the International Union of Crystallography s standard for representation of small molecules - and mmCIF [151], which is intended as a replacement for the PDB format for the representation of macromolecular structures, 

This section provides only a very brief overview of the file formats introduced above. Taking into account that the mmClF file format specifications alone already comprise about 1700 different entries [152], a detailed description of these file formats would occupy an entire book. 

PDB files were designed for storage of crystal structures and related experimental information on biological macromolecules, primarily proteins, nucleic acids, and their complexes. Over the years the PDB file format was extended to handle results from other experimental (NM.R, cryoelectron microscopy) and theoretical methods 

This rec ord/field terminology allows the treatment of a PDB file as an ordered collection of record types, 

All the records defined for PDB files can be grouped into six categories on the basis of how many times a given record can appear in a PDB file and how many lines it may occupy. 

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Besides the MDL Molfile formal, other file formats are often used in chemistry SMILES has already been mentioned in Section 2.3.3. Another one, the PDB file format, is primarily used for storing 3D structure information on biological macromolecules such as proteins and polynucleotides (Tutorial, Section 2.9.7) [52, 53). GIF (Crystallographic Information File) [54, 55] is also a 3D structure information file format with more than three incompatible file versions and is used in crystallography. GIF should not be confused with the Chiron Interchange Formal, which is also extended with. cif. In spectroscopy, JCAMP is apphed as a spectroscopic exchange file format [56]. Here, two modifications can be... 

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

The REMARK 4-999 records contain other optional, but predefined, remarks, As shown above, the "REMARK 4 record specifies that the analyzed file conform fully with, the current (December 2002) version 2.2 of the PDB file format specification. 

The Self-defining Text Archive and Retrieval (STAR) file format addresses primarily the problem of the inflexibility of the PDB file format, its fixed sets of allowable fields, and their strong dependence on order, To overcome the problems described, both the data. structure and the actual data items within a STAR file arc self-defined, which means that they are preceeded by corresponding names (labels) which identify and describe the data. The data may be of any type and there is no predefined order of the data. STAR files, in contrast to PDB files, are easy to read and write manually. The whole syntax of STAR files is very simple and is defined by only a few rules ... 

Data formats in the Brookhaven Protein Databank have become an intensively discussed topic in the last few years. The original PDB file format [17] was created in the late 1970s and maintained by the Research Collaboratory for Structural Bioinformatics [13]. In order to improve the organization of bibliographic... 

The first part of this section describes how this interpretation is done and which assumptions have been made to retrieve plausible results. The second part will then describe the algorithms used to compute bond characteristics from geometric information, because the PDB file format and its successors include no means to specify hybridization states or bond orders, which are essential for the characterization of properties of small organic ligands. Ligand bond characteristics interpretation is a prerequisite for the step to follow the detailed description of protein-ligand interactions by pharmacophore models. 

In the case of PDB ligands, only part of the graph information is defined in the PDB file format sepcification bond types and atom hybridization states are missing and will later be derived from the three-dimensional arrangement of connected atoms. Connectivity information, however, is already present and can be used to seperate cyclic from non-cyclic molecule parts. Especially for planar rings, this separation is a prerequisite for geometry interpretation, because of... 

PDB File Format Contents Guide, Version 2.2, 1996, available from the PDB consortium, Piscatway, NS and La Jolla, CA (www.pdb.org)... 

In contrast to the relational table design of mmCIF, the MMDB data records are structured as hierarchical records. In terms of performance, ASN.l-formatted MMDB files provide for much faster input and output than do mmCIF or PDB records. Their nested hierarchy requires fewer validation steps at load time than the relational scheme in mmCIF or in the PDB file format hence, ASN. 1 files are ideal for three-dimensional structure database browsing. 

Fig. 1.31 Conversion of a molfile of curcumin molecule to pdb file format in OpenBabel GUI...

Code for Getting the Protein Coordinates from PDB File Format (X, Y, Z values)... 

The PDB file format is governed by a published standard that is slowly changing to reflect the nature and quantity of data submitted. The current format is that of ASCII-encoded text partitioned into typed 80-character records. Only PDB files directly supplied by Brookhaven are assured of having all of these data properly formatted the PDB standard is manipulated by many third-party software developers as an interchange format, and extremely wide variations may be seen in both the canonical PDB record structure and overall PDB format One legitimate format variation is in support of entries with coordinates derived by solution NMR whereas the standard X-ray-derived PDB entry contains a single structure or conformer, the majority of NMR-derived PDB entries are ensemble collections of multiple conformers this provides access to the individual computed structures, but the format has proven troublesome to some third-party format translators. 

The PDB file format, originally developed for macro-molecular structures, but including capabilities for showing low-molecular-weight structures also. The PDB format is currently undergoing revision to provide compatibility with mmCIF. 

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