Three-dimensional data retrieval

Structure-activity relationships often allow the assignment of biological activity to a fragment of the parent molecule. Computer methods of chemical data-storage and retrieval allow such fragments to be identified in other compounds by si >-structure searches. It is also feasible to store three-dimensional data so that molecular models can be visu-ally compared and manipulated on oscilloscope screens. 

Another programming consideration is the effective use of the I/O channel between the ST-100 and the host. With a VAX host, the data transfer rates are less than 1 megabit/second. This precludes the possibility of having a fast system where the three-dimensional coordinates are transferred from the host to the ST-100 and the subsequently computed energies and forces retrieved from the ST-100 on every step. The GEMM package has been designed to minimize synchronous data transfers. In an ideal situation, the ST-100 runs without direction from the host, and data that need to be saved are streamed to the host while the ST-100 continues to produce new data. 

Martin, Y.C., Danaher, E.B., May, C.S., and Weininger, D. MENTHOR, a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by sub structural, biologic, physical, or geometric properties./. Comput.-Aided Mol. Des. 1998, 1, 15-29. 

The Structure of DNA Elucidation of the three-dimensional structure of DNA helped researchers understand how this molecule conveys information that can be faithfully replicated from one generation to the next. Tb see the secondary structure of double-stranded DNA, go to the Protein Data Bank website (www.rcsb.org pdb). Use the PDB identifiers listed below to retrieve the data pages for the two forms of DNA... 

For several years we have been involved in a wide-ranging project to develop methods for the representation and searching of the three-dimensional (3-D) protein structures in the Brookhaven Protein Data Bank [28, 29], Our work derives from the graph-theoretic methods that are used for the storage and retrieval of information pertaining to both two-dimensional (2-D) and 3-D small molecules [1, 58]. 

FIGURE 3.4.3 Cartoon representation of the three-dimensional structures of (a) Pru av 1 determined by NMR and (b) Api g 1 determined by x-ray crystallography. Pru av 1 represents an overlay of 22 chains retrieved from RCSB Protein Data Bank (accession number le09), Api g 1 (2bk0). Highly flexible loops between (33-(34 and (37-a3 structures are depicted in blue, (3-sheets in green, and a-helices in red. 

The Protein Data Bank (PDB http //www.pdb.org) is the worldwide repository of three-dimensional structural data of biological macromolecules, such as proteins and nucleic acids (Berman et al. 2003). The Protein Data Bank uses several text file-based formats for data deposition, processing, and archiving. The oldest of these is the Protein Data Bank format (Bernstein 1977), which is used both for deposition and for retrieval of results. It is a plain-text format whose main part, a so-called primary structure section, contains the atomic coordinates within the sequence of residues (e.g., nucleotides or amino acids) in each chain of the macromolecule. Embedded in these records are chain identifiers and sequence numbers that allow other records to reference parts of the sequence. Apart from structural data, the PDB format also allows for storing of various metadata such as bibliographic data, experimental conditions, additional stereochemistry information, and so on. However, the amount of metadata types available is rather limited owing to the age of the PDB format and to its relatively strict syntax rules. 

MENTHOR, A Database System for the Storage and Retrieval of Three-Dimensional Molecular Structures and Associated Data Searchable by Substructural, Biological, Physical, or Geometric Properties. 

The World Wide Web site of the Protein Data Bank at the RCSB offers a number of services for submitting and retrieving three-dimensional structure data. The home page of the RCSB site provides links to services for depositing three-dimensional structures, information on how to obtain the status of structures undergoing processing for submission, ways to download the PDB database, and links to other relevant sites and software. 

Links. PDB s search engine, the Structme Explorer, can be used to retrieve PDB records, as shown in Figure 5.2. The Structure Explorer is also the primary database of links to third-party aimotation of PDB structure data. There are a number of links maintained in the Structure Explorer to Internet-based three-dimensional structure services on other Web sites. Figme 5.2 shows the Structure Summary for the protein bamase (IBNR Bycroft et al., 1991). The Structure Explorer also provides links to special project databases maintained by researchers interested in related topics, such as structural evolution (FSSP Holm and Sander, 1993), structure-structure similarity (DALI Holm and Sander, 1996), and protein motions (Gerstein et al., 1994). Links to visualization tool-ready versions of the structure are provided, as well as authored two-dimensional images that can be very helpful to see how to orient a three-dimensional structure for best viewing of certain features such as binding sites. 

NCBI s Molecular Modeling Database (MMDB Hogue et al., 1996) is an integral part of NCBTs Entrez information retrieval system (cf. Chapter 7). It is a compilation of all the Brookhaven Protein Data Bank (Bernstein et al., 1977) three-dimensional... 

Entrez, to be clear, is not a database itself—it is the interface through which all of its component databases can be accessed and traversed. The Entrez information space includes PubMed records, nucleotide and protein sequence data, three-dimensional structure information, and mapping information. The strength of Entrez lies in the fact that all of this information can be accessed by issuing one and only one query. Entrez is able to offer integrated information retrieval through the use of two types of coimection between database entries neighboring and hard links. 

Storage and retrieval of two- and three-dimensional chemical structures with substructure search capability. Available chemical databases include ACD (available chemicals directory, >71,000 compounds), Derwent Standard Drug File (37,800 compounds). Drug Data Report (>20,000 compounds) and a pAa file (10,700 literature values). 

The segmentation procedure is repeated for each frame. Cross section frame data taken from an arbitrary but known position of the ultrasound transducer are transformed into their proper 3-D-coordinates and stored in a 3-D-database. This database is organized in a way to simplify retrieval processes. The combination of all stored cross section frames allows the three-dimensional reconstruction of the heart. Two approaches have been attempted ... 

In chemistry, four different types of library searching are important. They deal with four different types of chemical information, namely (1) textual and bibliographic information (e.g., literature citations, chemical names), (2) numeric data (e.g., physicochemical constants, biological data, test results), (3) chemical structures (e.g., three-dimensional molecular structures), and (4) spectroscopic data (e.g., representations of mass spectra, infrared spectra, and NMR spectra). The approaches and methods used for searching these types of libraries can differ dramatically depending on the size of the library, the purposes of the retrieval, the computer hardware and software available, the constraints that apply, such as necessary response time or memory size, and many other factors. 

Molecular Design Limited has recently extended their MACCS-II chemical database system to MACCS-3D, for the storage and retrieval of three-dimensional atomic coordinates. Physical and biological data may be stored. A novel feature of MACCS-3D is the ability to recognize and remove duplicate coordinate sets. Coordinate sets can be retrieved from the database by specifying a combination of numerical and textual queries or by substructure. 

Y. C. Martin, E. A. Danaher, C. S. May, and D. Weininger,/. Comput.-AidedMol. Design, 2, 15 (1988). MENTHOR, a Database System for the Storage and Retrieval of Three-Dimensional Molecular Structures and Associated Data Searchable by Substructural, Biologic, Physical, or Geometric Properties. 

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