Structure database records

This chapter introduces biomolecular structures from a hioinformatics perspective, with special emphasis on the sequences that are contained in three-dimensional structures. The major goal of this chapter is to inform the reader about the contents of structure database records and how they are treated, and sometimes mistreated, by popular software programs. This chapter does not cover the computational processes used by structural scientists to obtain three-dimensional structures, nor does it discuss the hner points of comparative protein architecture. Several excellent monographs regarding protein architecture and protein structure determination methods are already widely available and often found in campus bookstores (e.g., Branden and Tooze, 1999). 

This mental exercise helps to conceptualize what a three-dimensional structure database record ought to contain. There are two things that have been recorded here the chemical structure and the locations of the individual atoms in space. This is an adequate hmnan-readable record of the structure, but one probably would not expect a computer to digest it easily. The computer needs clear encoding of the associations of atoms, bonds, coordinates, residues, and molecules, so that one may construct software that can read the data in an imambiguous manner. Here is where the real exercise in structural bioinformatics begins. 

Molecular graphics visualization software performs an elaborate connect-the-dots process to make the wonderful pictures of protein structure we see in textbooks of biomolecular structure, like the structure for insulin (SINS Isaccs and Agarwa, 1978) shown in Figure 5.1. The connections used are, of course, the chemical bonds between all the atoms. In current use, three-dimensional molecular structure database records employ two different minimalist approaches regarding the storage of bond data. 

Biomolecular three-dimensional structure database records are cmrently not compatible with macroscopic software tools such as those based on CAD software. Computer-aided design software represents a mature, robust technology, generally superior to the available molecular structure software. However, CAD software and file formats in general are ill-suited to examine the molecular world, owing to the lack of certain specialty views and analytical functions built in for the examination of details of protein structures. 

Decide How Objects, Links, and Actions Are Implemented. This is highly dependent on the answers to the preceding question. Each component may have its own internal representation of objects as C structures, as Java or C++ objects, or as files or database records. Links may be memory addresses, URLs, CORBA identifiers, database keys, or customer reference numbers, or they may be refined to further objects. Actions may be further refined and ultimately be function calls, Ada rendezvous, signals, or Internet messages. 

DataBank Press it to visualize database records of compounds matching the current candidate structure. 

Figure 1. Structure of trans coniferyl alcohol and trans sinapyl alcohol (reproducedfrom reference 30. CAS Registry database records duplicated with permission of CAS, a division of the American Chemical Society).

Scientists that are unfamiliar with structure data often expect all structures in the public databases to be of textbook quality. They are often surprised when parts of a structure are missing. The availability of a three-dimensional database record for a particular molecule does not ever imply its completeness. Structural completeness is strictly dehned as follows At least one coordinate value for each and every atom in the chemical graph is present. 

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. 

The Cambridge Structural Database contains at least 16 records of imidazolium salts... 

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