Nucleic acid databases

Nucleic Acid Database http //ndbserver.rutgers.edu/NDB/... 

A systematic nomenclature has been developed for the chemokine receptors (see Table 1). Thus, receptors for CC chemokines are referred to as CCR, receptors for CXC chemokines as CXCR, and the receptors for the XC and CX3C chemokines as XCR and CX3CR, respectively. To date, there are 10 CCRs (CCRs 1 to 10), 7 CXCRs, a single XCR, and a single CX3CR. The numbering is based on the date of deposition of the chemokine receptor sequence within the nucleic acid databases. For orphan receptors, this date refers to the point of identification of the orphan receptors as chemokine receptors and not to the date of initial deposition in the cDNA databases. 

Table 2.4 The major primary sequence (protein and nucleic acid) databases and the web addresses from which they may be accessed...

Nucleation sites, in ferrosilicon, 22 516 Nucleation track membranes, 15 802 Nucleic acid bases, recognition of, 16 794 Nucleic Acid Database (NDB), 17 606 Nucleic acid probe assays, 16 380. See also DNA analysis Nucleic acid probes, 14 153 Nucleic acids, 17 602-643 20 444-447. See also Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)... 

The most widely used mass spectrometric identification procedure is MALDI-Tof analysis of the entire peptide mixture. Gas-phase matrix interaction with peptide ions in MALDI-Tof results in singly charged ions, giving a mass profile that is highly characteristic of the protein from which the peptides are derived. These peptide masses (actually protonated peptide molecular ions, MH+) can be used to search databases (either protein or nucleic acid databases) to identify the proteins. The two most important factors in successfully identifying proteins by this approach are the number of matching peptide masses and the accuracy of the peptide mass determination. 

Figure 12.4. Quick search for nucleic acid database at NBD. Search for the database can be performed by making choice(s) from the list(s) of pop-up box(es).

A. R. Srinivasan, B. Schneider, The nucleic-acid database - a comprehensive relational database of 3-dimensional structures of nucleic-acids. Biophys. J. 63, 751-759 (1992)... 

In fact, a tremendous amount of information is available on the structures of biological macromolecules descriptions of structures of proteins and nucleic acids make up major portions of modern textbooks in biochemistry and molecular biology. The Protein Data Bank and the Nucleic Acid Database are online archives that contain sequence and structural data on thousands of specific molecules and complexes of molecules. This structural information comes from in vitro experiments, with structures inferred from the x-ray diffraction patterns of crystallized molecules, spectroscopic measurements using multi-dimensional nuclear magnetic resonance, and a host of other methodologies. 

Biopolymer structnres are stored at the Protein Data Bank (PDB), founded in 1971 at Brookhaven National Laboratory (USA), and the Nucleic Acid Database (NDP), both currently operated by Rutgers, the State University of New Jersey (USA). As of April 2004, the PDB contained 25 176 structures and NDP had 2379 structures. 

Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh S-H, Srinivasan AR, Schneider B. The Nucleic Acid Database A comprehensive relational database 24. of three-dimensional structures of nucleic acids. Biophys. J. 1992 63 751-759. 

Nucleic Acids Database Structures of oligonucleotides and nucleic acids. 1,904... 

In this first section, we illustrate the performance of the GPW method on a desktop computer employing a single Pentium Xeon (3GHz) CPU for the calculations. The system studied is a dinucleoside monophosphate A2 p5 C that contains a 2-5 link, as opposed to the usual 3 -5 . The system has been crystallised and discussed in detail in [31]. Its structure is available in the nucleic acid database [4] under entry URBOOl. It crystallises with an orthorhombic unit cell (8.631 A by 18.099 A by 16.101 A) with space group... 

NLM Gateway NMR Shift DB Nucleic Acid Database Particle Data Group Physical Property Information... 

The Atlas of Nucleic Acid-Containing Structures from the Nucleic Acid Database Project http //202.213.175.il/ NDB/NDBATLAS/index.html offers a similar range of... 

Table 4.2 lists some examples of structural parameters that vary between dinucleotides [15, 16]. Despite the fact that there are some 700 structures of nucleic acids in the Nucleic Acid Database and Protein Data Bank [14], there are not enough structures to give good statistics on trinucleotide or tetranucleotide steps in other words, the context dependence of these structural parameters is still being examined [16], which accounts in part for the large range of values for certain of the parameters in Table 4.2. 

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