Databases biochemical

Many biological databases (databanks) are embedded with tutorials that make it easy to explore their facilities. There are three sources of biological databases in-house dedicated sources (private and limited for focused projects), databases assembled by companies (mainly fees for services extensive and high-quality but expensive and restrictive such as Celera Genomics and Incyte Genomics), and public databases (such as GenBank, EMBL and DDBJ). An important distinction exists between primary (archival) and secondary (curated) databases. The primary databases represent experimental results with some interpretation (Table 14.11). Their record is the sequence or structure as it was experimentally derived. 

Primary data collections related to biomolecules include  

TABLE 14.11 Some primary database sites of biochemical interest 

NCBI Sequence structure resources http //www.ncbi.nlm.nih.gov 

Protein Information Resource (PIR), Intemat l http //pir.georgetown.edu/ 

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Many biochemical databases with sophisticated topics have been developed for solving various problems. Since 1996 the first issue of each journal volume of Nucleic Acid Research has been reserved for the presentation of molecular biology databases [28]. A comprehensive catalog on the Internet is DBCAT, currently listing 511 databases [29, 30). 

In particular, Eq. (Ill) allows us to make use of existing biochemical databases and known dissociation constants (see Section III.D). Sometimes it is useful to rewrite Eq. (Ill) in terms of a (measured or assumed) metabolic steady state S° and v° in particular, given the progress in experimental accessibility of system variables discussed in Sections IV and VI. In this respect, an appropriate reparameterization is obtained straightforwardly by adjusting the product ETk+ to yield Vj(S°,/>0) = v . 

Most biochemical databases request the user to enter keywords to search/retrieve information concerning biomolecules (unless the identifiers of the compounds are known). The keyword is normally the IUBMB (International Union of Biochemistry and Molecular Biology) name or common name of the compound. In particular, the linkage and conformational designations of oligomeric compounds needs to be specified. The IUBMB nomenclature for biochemical compounds can be accessed from the IUBMB site at http //www.chem.qmw.ac.uk/iubmb/. Some useful databases for biochemical compounds are listed in Table 5.3. 

For a comprehensive catalog of biochemical databases, Dbcat (Discala et al 2000) at http //www.infobiogen.fr/services/dbcat/ should be consulted. 

While an OOP representation is flexible, it nonetheless encompasses an overall view, i.e., the designer s vision of the general nature (but not the details) of the computational methods that will rely on the representation. Here, the scope envisioned for the representation of biochemical pathways is defined to include the following general goals. The system should function as a biochemical database, allowing the storage and retrieval of commonly available types of data for biochemical compounds, reactions, pathways, and enzymes. For each type of object, a different set of data must be available and easily accessible,... 

TOXCENTER TOXCENTER on STN is a bibliographic database that covers the pharmacological, biochemical, physiological, and toxicologicitl effects of drugs and other chemicals. The data m TOXCENTER are from 1907 to the preseni, Tliere are more Ihan 5,7 million records (December, 2002). It is updaled weekly... 

Besides such textual databases that provide bibhographic information, sequence databases have attained an even more important role in biochemistry. Sequence databases are composed of amino add sequences of peptides or proteins as well as nudeotide sequences of nudeic acids. The 20 amino adds are mostly represented by a three-letter code or by one letter according to the biochemical conventions) the four nudeic adds are defined by a one-letter code. Thus the composition of a biochemical compound is searchable by text retrieval methods. 

What is needed for progress in achieving a deeper insight into biochemical pathways is to allow all this information to be searchable by electronic means in other words, it has to be stored in a reaction database. 

The tutorial in Section 10.3.1.8 presents some of the various ways the information in the Biochemical Pathways database can be retrieved. In this tutorial the importance of searching for the reaction center, the atoms and bonds directly involved in the bond rearrangement scheme, is emphasized, It is a prerequisite for getting a deeper understanding of chemical reactions. 

The reaction database compiled on Biochemical Pathways can be accessed on the web and can be investigated with the retrieval system C ROL (Compound Access and Retrieval On Line) [211 that provides a variety of powerful search techniques. The Biochemical Pathways database is split into a database of chemical structures and a database of chemical reactions that can be searched independently but which have been provided with efficient crosslinks between these two databases. 

The 3D pharmacophore search with C(5)ROL in the Biochemical Pathways database provided 13 different molecules as hits. To further limit the number of hits, the additional restriction was imposed that the hits should have only two hydrogen... 

These examples served to show that the Biochemical Pathways database provides a rich source of information on these all important reactions that determine the transformation of nutrients into the broad spectrum of compounds contained in living species and the concomitant production of energy to keep these processes going. 

GD Schuler. Sequence alignment and database searching. Methods Biochem Anal 39 145-171, 1998. 

Incorporating the Kirtas system with the International Plant Names Index and SNOW-MED allows movement of the historic text into an electronic format, identihcation of current plant names, and identihcation of the symptoms treated with the plants. To complete the mining of historic herbal texts for novel drug leads we use the Natural Products Alert (NAPRALERT ) database to compare the information extracted from the historic herbal text to the reports of plant use in the current literature. The NAPRALERT database provides a summary of plants ethnopharmacological use, biochemical activities, and isolated compounds [27]. By querying each plant (with the current plant name) it is possible to identify any reports in the current literature regarding the plant. As an example, Table 4.1 shows the NAPRALERT output for Cycas rumphii. 

Patnaik SK, Blumenfeld OO Use of on-line tools and databases for routine sequence analyses. Anal Biochem 2001 289 1. 

To ensure microbial strains are viable and pure a suite of morphological, biochemical, and cytochemical tests are used to confirm characteristics specific to their taxons. A number of commercially available rapid identification kits are also employed for some common genera. In addition to these taxon specific tests, many of the cultures are tested for their fatty acid methyl ester (FAME) profiles using the commercial MIDI system. The FAME profiles can be compared to the MIDI database for species identification/confirmation purposes. The Biolog system, which yields a metabolic fingerprint of an organism, is another alternative for rapid identification. 

There are many situations in which scientists need to know how alike a number of samples are. A quality control technician working on the synthesis of a biochemical will want to ensure that each batch of product is of comparable purity. An astronomer with access to a large database of radiofrequency spectra, taken from observation of different parts of the interstellar medium, might need to arrange the spectra into groups to determine whether there is any correlation between the characteristics of the spectrum and the direction of observation. 

Classifier systems are software tools that can learn to control or interpret complex environments without help from the user. This is the sort of task to which artificial neural networks are often applied, but both the internal structure of a classifier system and the way that it learns are very different from those of a neural network. The "environment" that the classifier system attempts to learn about might be a physical entity, such as a biochemical fer-mentor, or it might be something less palpable, such as a scientific database or a library of scientific papers. 

The time-resolved aspect of domino processes would, however, be in agreement with cascade reactions as a third expression used for the discussed transformations. Unfortunately, the term cascade is employed in so many dilferent connections - for example, photochemical cascades, biochemical cascades or electronic cascades - on each occasion aiming at a completely dilferent aspect, that it is not appropriate moreover, it also makes the database search much more difficult Moreover, if water molecules are examined as they cascade, they are simply moving and do not change. Several additional excellent reviews on domino reactions and related topics have been published [7], to which the reader is referred. 

Altschul, S. F.andKoonin, E. V.(1998), Iterated profile searches with PSI-LAST - a tool for discovery in protein databases, Trends Biochem. Set ( Computer Corner ), 23, 444-446. 

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