Domains PRINTS

PPP (point-to-point protocol) primary domain print queue... 

The functional microarray typically consists of a collection of full-length functional proteins or protein domains printed on glass slides that are then exposed to a protein preparation from a cell that represents the entire proteome of that cell. This method is useful in determining protein-protein interactions. In addition, this method is useful in predicting the interaction of proteins with DNA, RNA, phospholipids, and small molecules. RPA includes glass slides on which a cellular protein preparation is fixed and then probed with a known antibody. This method helps in identifying the proteins that are altered and cannot bind with a known antibody in the proteome of diseased cell types. This method also identifies the proteins that are altered as a result of phosphorylation or other posttranslational modifications in normal and disease conditions or under growth conditions. 

Fig. 10.4. (Opposite) Alignments of nematode chitinases with the active centre boxed. Identical amino acids are marked with an asterisk ( ) similar amino acids are marked with a dot (.). Conserved cysteine residues in the chitin-binding domain are printed in bold. Gene Bank accession numbers C.eleg. Chit (C. elegans), Q11174 OvL3 Chit (O. volvulus), L42021 AvL3 Chit (A viteae), U14638 B.m. Chit(B. malayi), M73689.

Figure 7.32 Apo form of metal binding domain 4 of Menkes copper-transporting ATPase described in reference 133 (PDB 1AW0). Visualized using Wavefunction, Inc. Spartan 02 for Windows . See text for visualization details. Printed with permission of Wavefunction, Inc., Irvine, CA. (See color plate.)...

It can be difficult if not impossible to find the domain structure of a protein of interest from the primary literature. The sequence may contain many common domains, but these are usually not apparent from searches of literature. Articles defining new domains may include the protein, but only in an alignment figure, which are not searchable. Perhaps, with the advent of online access to articles, the full text including figures may become searchable. Fortunately there have been several attempts to make this hidden information available in away that can be easily searched. These resources, called domain family databases, are exemplified by Prosite, Pfam, Prints, and SMART. These databases gather information from the literature about common domains and make it searchable in a variety of ways. They usually allow a researcher to look at the domain organization of proteins in the sequence database that have been precalculated and also provide a way to search new sequences... 

Figure 2.21 Zinc coordination sphere in a zinc-finger protein from the synthetic construct corresponding to Xenopus Xfin-31 domain from PDB IZNF. Visualized using The PyMOL Molecular Graphics System and ChemDraw Ultra, version 10.0. (Printed with permission of Delano Scientific, LLC and CambridgeSoft Corporation)...

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It performs information embedding in the spatial domain and hence is sensitivity to geometric deformation such as image miss-alignment and to the presence of stains or scribbles on the printed media. 

Prior art is that information which was available in the public domain at the time of the production of the data on the invention. The search for prior art is therefore not just the relatively simple matter of checking the literature for conflicting patents. It also involves a detailed search of the literature for any piece of information that discloses any aspect of the invention. Such disclosures include not only patents but also any printed article or oral presentation, sales literature, offers for sale or actual sale of materials, which have been made publicly available. This is a time consuming activity but one which is necessary since it can avoid spurious applications being made which are later rejected by the Patent Office. Additionally, under the law the applicant has a duty to disclose all prior art that can have reasonably been known to exist. 

From preprint servers 319 Ward, D. W. Nelson, K. A. Finite Difference Time Domain (FDTD) Simulations of Electromagnetic Wave Propagation Using a Spreadsheet. 2004,arXiv physics/0402096.arXiv.org e-Print archive, http //arxiv.org/abs/physics/0402096 (accessed Oct 13,2004). 

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