Structure data base interfaces

The PHRAN-SPAN natural language interface for system-level specifications, the AGIS graphics interface for directly manipulating the Design Data Structure, the 3DIS data base interface, and the SLIDE hardware description language. 

Once many in-house, chemical structure data bases had been built, the users began to realize that it was more efficient to use commercially-available structure handling software for structures alone (or structures and a minimal amount of related property data) and to take advantage of data base management systems to handle property data. Molecular Design Limited (MDL) and Telesystemes modified their MACCS and DARC software, respectively, to allow for the appropriate interfacing of structures and data. 

CAMPUS uses a uniform database structure and uniform interface for all participating suppliers, with frequent updates of the property data. It allows preselection or screening of materials, suitable for specific applications, from a worldwide range of commercial plastics, while continuously being developed further with respect to its properties base. CAMPUS is based on two international standards for comparable data, that use meaningful properties based on unambiguous selection of specimen types... 

It is emphasized that revealing the dynamics as well as the structure (or conformation) based on several types of spin-relaxation times is undoubtedly a unique and indispensable means, only available from NMR techniques at ambient temperature of physiological significance. Usually, the structure data themselves are available also from X-ray diffraction studies in a more refined manner. Indeed, better structural data can be obtained at lower temperature by preventing the unnecessary molecular fluctuations, which are major subjects in this chapter, since structural data can be seriously deteriorated for domains where dynamics are predominant even in the 2D or 3D crystalline state or proteoliposome at ambient temperature. It should be also taken into account that the solubilization of membrane proteins in detergents is an alternative means to study structure in solution NMR. However, it is not always able faithfully to mimick the biomembrane environment, because the interface structure is not always the same between the bilayer and detergent system. This typically occurs in the case of PLC-81(1-140) described in Section 4.2.4 and other types of peptide systems. 

Visual basic-based interface and knowledge base Object oriented system implemented in C++ Implemented as a conventional structured program Object-oriented program using lab data and numerical relationships Object-oriented expert system implemented in C++ interfacing with a database on materials and compositions... 

Chapter 1 summarizes methods for the stabilization of artificial lipid membranes. They include synthesis of new types of polymerizable lipids and polymerization of membranes. Creation and characterization of novel poly(lipid) membrane systems, as well as their functionalization for biotechnological applications, are also described. Chapter 2 addresses experimental studies on the design and characterization of lipopolymer-based monolayers at the air-water interface. Thermodynamic and structural data collected with X-ray and neutron reflectrometry, infrared reflection absorption spectroscopy, and sum frequency generation spectroscopy provide... 

Of the many X-ray based techniques available, a very powerful approach for probing interfacial structures is based on the measurement of X-ray reflectivity. The X-ray reflectivity is simply defined as the ratio of the reflected and incident X-ray fluxes. In the simple case of the mirror-like reflection of X-rays from a surface or interface, i.e., specular reflectivity, the structure is measured along the surface normal direction. Lateral structures are probed by non-specular reflectivity. The measurement and interpretation of X-ray reflectivity data (i.e., the angular distribution of X-rays scattered elastically from a surface or interface) (Als-Nielsen 1987 Feidenhans l 1989 Robinson 1991 Robinson and Tweet 1992) are derived from the same theoretical foundation as X-ray crystallography, a technique used widely to study the structure of bulk (three-dimensional or 3D) materials (Warren 1990 Als-Nielsen and McMorrow 2001). The immense power of the crystallographic techniques developed over the past century can therefore be applied to determine nearly all aspects of interfacial structure. An important characteristic of X-ray reflectivity data is that they are not only sensitive to, but also specifically derived from interfacial structures. 

The cyclization mechanism of type 11 terpene cyclases is exemplified by the reaction of the SHC (Scheme 87.19). Important insights into the reaction mechanisms have been obtained from structural data [199, 208]. One of the inner helices of the p-domain of SHC contains a conserved DxD(D,E) motif that is located in the central cavity at the interface between the p- and y-domains. Its central aspartate residue D376 is polarized via hydrogen bonding to an adjacent histidine residue and protonates the double bond of the squalene substrate to initiate the reaction cascade. Conserved aromatic residues stabilize the intermediate cations by cation-tt-interactions. A water molecule is a candidate to act as catalytic base, and this water may also account for the formation of the by-product hopanol. Another bridging water molecule connects D376 to a tyrosine residue and can restore the active site after catalysis by reprotonation of D376. 

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