Database Structures File

The connection table of the query object (similarity probe) is processed to obtain the set of atom pairs, and then the database file is scanned to evaluate the similarity between the query and each of the database structures. The maximum number of structures that the program will select is specified, as well as the minimum similarity score that a database compoimd must show to be selected. Within these limits, the program will select from the database the structures that are most similar (with the highest similarity value) to the query and will create an output file of compoimd numbers and similarity values, sorted by decreasing similarity, for the selected compounds. 

SD structure file or a file containing a list of identification numbers [Excel or Comma Separated Value (CSV) format] can be uploaded. In the Excel or CSV cases the protocol will automatically look up the structure that corresponds to the identification number, as it does for the text box input. A useful feature (see Databases under Parameters in Fig. 7) is the ability to search multiple databases in a single search. This is made possible by the use of Perl in the Pipeline Pilot protocol. The Perl code is very general and easily allows for the addition of new databases as they become available, thereby further increasing the versatility of this protocol. 

The 3D Structure files of ell published molecules ai held in the Pratein Date Bank (PDB), an online resource for researchers, educators, and the general public. Every structure file in this international database is identified by a four character ID cads. 

Figure 2.150. Ligprep is used for the rapid conversion of 2D structure files into accurate 3D models suitable for use in database screens and other applications. At the user s discretion Ligprep can generate multiple protonation states, enumerate chiralities, and generate tautomeric forms of the ligand...

To facilitate the validation process on the basis of the above approach, the MS electronic data is contributed to the OPCW Laboratory in any of the following electronic formats JCAMP, NIST ASCII, AMDIS, and NIST MS Database. Contributing laboratories provide mostly the NIST MS Database format, with structures. The OPCW Code and the Schedule number are placed in the synonym field of the database. The file is submitted to the OPCW Laboratory either as the NIST MS User Database or the corresponding set of text files representing the MSP (Spectral) and MOL (Structure) information. The NIST MS Search/Analysis programs are used for the management of the MS electronic data and also GC(RI) once merged with the MS data. 

Module relationships (events, timers, handshaking) Database schema File structures System interfaces... 

Pre-1980 —Flat File Storage of Chemical Structures. Computers consisted of mainframe machines (e.g., IBM 3090) and small minicomputers (Digital, Prime). Users connected through low speed serial connections, using "dumb" terminals (no graphics capability) or monochrome vector graphics terminals such as Tektronix and Imlac. Chemical structures were mainly stored as either (l)individ-ual structure files, indexed by name, and handled one or a few structures at a time or (2) in a flat-file database accessed by record number (26). A typical corporate database contained up to a few tens of thousands of structures. 

Flat Database or File. Essentially a spreadsheet of data, in which a given row contains all the data about a structure. There are no hierarchical relationships in a flat database. Many older and proprietary structure databases were flat in structure. These are in contrast to relational databases that are more commonly used at present. 

Registry Number. A unique identifier assigned to a chemical structure or other piece of data when it is registered into a database. The registry number may be internal, primarily for use by the database search system, or external, to be used by chemists and to link the data to other databases and files. 

The National Cancer Institute (NCI) database is a freely available collection of more than 200,000 compounds and it is frequently used by research groups to perform virtual screening followed by experimental testing. Table 2.2 contains two links where it is possible to mine the database online and to download structure files for analysis. 

New SQL functions and data types can be used to extend a relational database. This is explained in Chapter 10 using PostgreSQL as an example. Ways in which three-dimensional molecular structures can be stored are examined in Chapter 11. This chapter also advocates using an RDBMS instead of molecular structure files and shows how this transition might be accomplished. 

Chapter 13 shows sample applications that might be developed to produce a registry of compounds for use within a company or project. A set of utility functions is discussed that allows molecular structure files to be imported into a database and used in various ways. 

The previous section shows how molecular structures stored in an RDBMS can be made available to client programs that traditionally read molecular structure files. The advantage of storing molecular structures in an RDBMS is that the information can be used from within the database, as well as by external clients. For example, it would be possible to search a table of molecular structures for three-dimensional overlap, much like it might be searched for substructure match. Of course, such search functions need to be written and installed as extensions to an RDBMS, just like the matches functions was done for substructure searches. This section shows some possible ways this might be accomplished. 

National Cancer Institute. Downloadable structure files of NCI open database compounds. 2007. http //cactus.nci.nih.gov/ncidb2/download.html (accessed April 18,2008). 

Today, I have turned my habit around. When I have a set of chemical structures or data files, my first task is to organize them in a relational database. After all, the tools I now use are designed to read and write tables in a database. Rather than creating folders to keep project files, I create a schema of tables with rows holding chemical structures and data imported from the files. For example, the PubChem project provides information on millions of compounds in the form of hundreds of chemical structure files and associated experimental data files. While PubChem provides excellent Web tools to search this data, for local use I developed a schema to hold the structures and data in related tables. One possible schema for this is shown in Chapter 6 of this book. 

Database schema File structures System interfaces... 

Application Configuration Specification. The Application Configuration Specification (ACS) documents the application configuration required to meet the URS. The ACS records system setup parameters, process configuration, database configuration, file structures and so on required to implement the specific business implementation of the system. Where a standard implementation of the core product is adopted, this will be the only custom specification delivered to the pharmaceutical organization, accompanied by standard technical and user manuals. 

The projected, numerical factual database BEILSTEIN-ONLINE represents a natural extension of the Beilstein Handbook of Organic Chemistry which has been published for more than 100 years in more than 300 volumes. The Handbook together with the structure file cards of the literature period 1960-1980 (E-V Period) contain factual and structural information on more than 4 million compounds. The computer representation of organic chemical structures therefore constitutes the centre part of the database design. The chemical structure is described in a post-topological format. Not only constitutional information is included but also a complete stereochemical representation. Bond orders are replaced by electronic information. This allows a much more global and unique representation of tautomers. This paper gives an overview not only of the data structure of chemical compounds but also of its associated physical numerical data and keywords. 

The structure of the database can be divided into two parts the numeric factual file and the structure file (Figure 2). These two parts are subsequently described in more detail. 

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