PDB Files

At present, the data base used for the fit was not specially selected to avoid homologous proteins. Thus, a further improvement can be expected from using data for one of the specially prepared lists of PDB files (cf. Hobohm et al. [9]). We also expect further improvements from replacing the polynomial fits in the potential estimation procedure by piecewise cubic fits though at the moment it is not clear how to select the number of nodes needed to get a good but not overfitting approximation to the density. Finally, we are considering... 

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... 

PDB file. pdb Protein Data Bank file format for 3D stmcture information on proteins and polynucleotides nmm.rcsb.org 53... 

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. 

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. 

Each record in this category can appear only once in a PDB file and it occupies exactly one line. Examples of such records arc HEADER - the starting record of each PDB file discussed in detail below, END - the last (terminating) record, and CRYSTl - describing the crystallographic cell. 

All the records constituting a PDB file must appear in a strictly defined order, collected into sections, The order of the sections, together with a short description and sample record names, is presented in Thble 2-7 (source Ref. [33]). 

Having looked at the general structure of PDB files, let us now examine a sample PDB file. The file represents the structure of r conotoxin PNll polypeptide (PDB ID Ipcn) and was retrieved from the Protein Data Bank [53]. Figure 2-109 shows the 3D structure of the molecule. 

Representation of Chemico Compounds ll5 Table 2-7. Ordered list of sections in PDB files (souce Ref [53 ). 

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. 

Figure 2-112. Primary structure and heterogen sections of the analyzed PDB file.

As this short example shows. PDB files use different syntax for different records and both writing and reading such files require much effort. Another problem is the extensibility of this format to handle new kinds of information, which further complicates the file structure. The Protein Data Bank has been faced with the consequences - the existing legacy data comply with several different PDB formats, so they are not uniform and they arc more difEcuh to handle (145, 155, 157]. As mentioned in Section 2,9.7.1, there is a much more flexible and general way of representing molecular structure codes and associated information - the STAR file format and the file formats based on it. 

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 ... 

Molfile, SDfile, and PDB-file are the most popular data exchange formats. 

Select Brookhaven (PDB) Files from Hie List files of type menu, and then open the file water. pdb, located in the quick subdirectory. 

In chapter 2 I gave you the. pdb file which contains the Cartesian coordinates. We just add a couple of records to define the level of theory (HF/STO-3G), the charge (0) and spin multiplicity (1). 

The water-soluble fragment of the Rieske protein from bovine heart bci complex (ISF) was crystallized by Link et al. (30) and the structure was solved at 1.5 A resolution by Iwata et al. (9) (PDB file IRIE). 

Fig. 2. Ribbon diagram of the structures of (a) the water-soluble Rieske fragment from bovine heart bci complex (ISF, left, PDB file IRIE), (b) the water-soluble Rieske fragment from spinach b f complex (RFS, middle, PDB file IRFS), and (c) the Rieske domain of naphthalene dioxygenase (NDO, right, PDB file INDO). The [2Fe-2S] cluster is shown in a space-filling representation, the ligands as ball-and-stick models, and residues Pro 175 (ISF)/Pro 142 (RFS)/Pro 118 (NDO) as well as the disulfide bridge in the ISF and RFS as wireframes.

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