Interaction data bases

BIND Biomolecular Interaction Data Base, which is designed to store full descrip-... 

Su, C., J. M. Peregrin-Alverez, G. Butland, S. Phanse, V. Fong, A. Emili, and J. Parkinson. 2008. Bacteriome.org—an integrated protein interaction data base for E.coli. Nucleic Acids Res. 36, 334-336. 

The data base contains provisions for a simple augmentation by up to eight additional compounds or substitution of other compounds for those included. Binary interaction parameters necessary for calculation of fugacities in liquid mixtures are presently available for 180 pairs. 

An important approach to the graphic representation of molecules is the use of a connection table. A connection table is a data base that stores the available bond types and hybridizations for individual atoms. Using the chemical formula and the connection table, molecular stmctures may be generated through interactive graphics in a menu-driven environment (31—33) or by using a linear input of code words (34,35). The connection table approach may be carried to the next step, computer-aided molecular design (CAMD) (36). 

Aside from the fundamentals, the principal compromise to the accuracy of extrapolations and interpolations is the interaction of the model parameters with the database parameters (e.g., tray efficiency and phase eqiiilibria). Compromises in the model development due to the uncertainties in the data base will manifest themselves when the model is used to describe other operating conditions. A model with these interactions may describe the operating conditions upon which it is based but be of little value at operating conditions or equipment constraints different from the foundation. Therefore, it is good practice to test any model predictions against measurements at other operating conditions. 

While the data provide clear evidence for the formation of incomplete oxidation products, and help to identify the nature of the stable adsorbate(s) formed upon interaction with the respective Ci molecules, the molecular-scale information on the actual reaction mechanism and the main reaction intermediates is very indirect. Also, the reaction step(s) at which branching into the different reaction pathways occurs (e.g., direct versus indirect pathway, or complete oxidation versus incomplete oxidation) cannot be identified directly from these data. Nevertheless, by combining these and the many previous experimental data, as well as theoretical results, conclusions on the molecular-scale mechanism are possible, and are substantiated by a solid data base. 

The laser disk, a catalog of the entrees, a computer data base, and selected interactive programs can be obtained from Dr. Wayne Crowell, Dept, of Veterinary Pathology, University of Georgia, Athens, GA 30602. 

Using the same data base of all children from all clinics, there were no statistically significant interaction effects found, wherein differences between blends depended on the nutrition... 

Let us show some possible explanations of such experimental data based on the application of spatial-energy concepts. As before we will consider the approximate equality of effective energies of interacting subsystems as the main condition for the formation of stable structure based on the following equation ... 

Some other theoretical aspects of ionic solvation have been reviewed in the last few years. The interested reader is referred to them ionic radii and enthalpies of hydration 20>, a phenomenological approach to cation-solvent interactions mainly based on thermodynamic data 21>, relationship between hydration energies and electrode potentials 22>, dynamic structure of solvation shells 23>. Brief reviews, monographs, and surveys on this subject from a more or less different point of view have also been published 24—28) ... 

Automate Declslon-maklng Process. For dally operation, TOGA Is run automatically from gas chromatograph output and data bases (as opposed to Interactively) to generate expert Interpretation of data, this speeds up the data analysis task and removes the element of human error from routine diagnoses. 

Such a system would include a program similar to that of Storer and Comish-Bowden to do equilibrium calculations. A communication-control subprogram would be Hiked to an expert model by using the EXPERT knowledge-base shall (or system-builder) which is advantageous here because it can interact with procedures such as those written in FORTRAN for numerical computation. Additional programs and a small data base, which EXPERT can handle, would keep track of which chemical was what array element, and other requirements mentioned above. 

Specific research subjects have emerged with respect to improved descriptions of specific phenomena. Some time ago, it was speculated that gas-solid interactions and turbulence effects on reaction kinetics would be important areas of advance in the modeling art. Gas-solid interactions include both chemical formation of aerosols and reactions on surfaces of pre-existing suspended particulate matter. Because of differing effects of a material in the gas phase and in some condensed phase, it will be important to characterize transformation processes. The achex (Aerosol Characterization hYperiment) program recently carried out under the direction of Hidy will provide an extensive data base with which to test new ways of treating the gas-solid interaction problem. 

The method preferred in the NBA Thermochemical Data Base review is the specific ion interaction model in the form of the Bronsted-Guggenheim-Scatchard approach. 

The specific ion interaction approach is simple to use and gives a fairly good estimate of activity factors. By using size/charge correlations, it seems possible to estimate unknown ion interaction coefficients. The specific ion interaction model has therefore been adopted as a standard procedure in the NEA Thermochemical Data Base review for the extrapolation and correction of equilibrium data to the infinite dilution standard state. For more details on methods for calculating activity coefficients and the ionic medium/ ionic strength dependence of equilibrium constants, the reader is referred to Ref. 40, Chapter IX. 

Planet is a Cabinet server that provides information about protein-ligand interactions. Data are read in the PDB format for observed or hypothetical interactions. Each data object is a relationship between a protein and one or more ligands and other small molecules (cofactors, etc.). Several specific relationships are explored the relationships between small and big molecules, between protein chain residues and relationships based on EC numbers. 

Diffraction analysis—whether employing x-rays, electrons, or neutrons—is the method of choice for obtaining structural information on crystalline substances. The application of the well understood principles and methods of diffraction analysis to single crystals of sufficient size and perfection can lead to a detailed determination of the crystal structure, without recourse to any auxiliary methodology. Hundreds of mono- and oligosaccharide molecules have been characterized by these means (1), yielding not only an increased understanding of their structures in the solid state, but also a data base useful for extrapolation to other states and molecular interactions. 

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