Nucleic Acid Database Project

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... 

F. Desiere, et al., The PeptideAtlas Project. Nucleic Acids Res., 34, Database issue (2006) D655-D658. 

FlyBase (1999) The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Research 27, 85-88. 

Solovyev V. V., Salamov A. A. (1999) INFOGENE a database of known gene structures and predicted genes and proteins in sequences of genome sequencing projects. Nucleic Acids Res.,... 

Bernal, A., Ear, U., and Kyrpides, N. (2001) Genomes OnLine Database (GOLD) a monitor of genome projects world-wide. Nucleic Acids Res. 29, 126-127. 

Explicit sequences in a PDB hie are provided in lines starting with the keyword SEQRES. Unlike other sequence databases, PDB records use the three-letter amino acid code, and nonstandard amino acids are found in many PDB record sequence entries with arbitrarily chosen three-letter names. Unfortunately, PDB records seem to lack sensible, consistent rules. In the past, some double-helical nucleic acid sequence entries in PDB were specihed in a 3 -to-5 order in an entry above the complementary strand, given in 5 -to-3 order. Although the sequences may be obvious to a user as a representation of a double helix, the 3 -to-5 explicit sequences are nonsense to a computer. Fortunately, the NDB project has hxed many of these types of problems, but the PDB data format is still open to ambiguity disasters from the standpoint of computer readability. As an aside, the most troubling glitch is the inability to encode element type separately from the atom name. Examples of where... 

BL Maidak, N Larson, MJ McCaughey, R Overbeek, GJ Olsen, K Eogel, J Blandy, CR Woese. The ribosomal database project. Nucleic Acids Res 22 3485-3487, 1994. 

Protein-ligand interactions are important phenomena that touch upon every facet of biological functions. These include such examples as enzyme-substrate interactions in biochemical transformations, transducer-membrane interactions in signal transduction, protein-nucleic acid interactions in genetic transmission, protein-carbohydrate interactions in cell adhesion as well as protein-protein interactions in biochemical regulations and defense (immune response). Databases of interacting proteins are available respectively at DIP (http //dip.doe-mbi.ucla.edu) and IntAct project of EBI (http //ebi.ac.uk/intact). 

Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. Ribosomal Database Project data and tools for high throughput rRNA analysis. Nucleic Acids Res 2014 42(D1) D633-D642. 

Cole, J.R., Chai, B., Farris, R.J., Wang, Q. et al.. The Ribosomal Database Project (RDP-II) sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res., 33, D294—D296 (2005). 

The FlyBase Consortium 1999. The FlyBase Database of the Drosophila Genome Projects and Community Literature. Nucleic Acids Res. 27 85-88. 

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