Prediction of structures

Bolotin, V. V. 1994 Fatigue Life Prediction of Structures. In Spanos, P. D. and Wu, Y. (eds). Probabilistic Structural Mechanics Advances in Structural Reliability Methods. Berlin Springer-Verlag. 

Sternberg, M.J.E., et al. Analysis and prediction of structural motifs in the glycolytic enzymes. Phil. Trans. 

The presentation of the rearranging intermediates as mesoionic ground-state species (196) and (199) has proved an adequate tool for the prediction of structural changes in this field. The steric factors which direct the partly selective rearrangement paths of the bicyclohexenone and dienone photoisomers of (174) and their corresponding alkylated homologs have been extensively discussed in a recent review by this author. ... 

In general the relevance of predictions of structure-function relationships based on molecular modeling and structural bioinformatics are threefold. First they can be used to answer the question of which partners (proteins) could interact. Second, predictions generate new hypotheses about binding site, about molecular mechanisms of activation and interaction between two partners, and can lead to new ideas for pharmacological intervention. The third aim is to use the predictions for structure-based drug design. 

As an illustration of the application of the principles in the prediction of structures with the coordination theory, some properties of the structures of the three forms of Al-iSiOs, cyanite, andalusite and sillimanite, are predicted. 

Molecular mechanics calculations have become a well established tool in the area of coordination chemistry, including the coordination chemistry of nickel375-379 where they are often applied for the analysis or the prediction of structures,380 the computation of isomer or conformer ratios and metal ion selectivities,381,382 and for simulating spectroscopic properties in combination with AOM calculations or by hybrid quantum mechanics/molecular mechanics (QMMM) methods.383,384 Details of the various approaches, e.g., the incorporation of d-electron stabilization energy... 

In the investigations of molecular adsorption reported here our philosophy has been to first determine the orientation of the adsorbed molecule or molecular fragment using NEXAFS and/or photoelectron diffraction. Using photoemission selection rules we then assign the observed spectral features in the photoelectron spectrum. On the basis of Koopmans theorem a comparison with a quantum chemical cluster calculation is then possible, should this be available. All three types of measurement can be performed with the same angle-resolving photoelectron spectrometer, but on different monochromators. In the next Section we briefly discuss the techniques. The third Section is devoted to three examples of the combined application of NEXAFS and photoemission, whereby the first - C0/Ni(100) - is chosen mainly for didactic reasons. The results for the systems CN/Pd(111) and HCOO/Cu(110) show, however, the power of this approach in situations where no a priori predictions of structure are possible. 

SNP/mutation functional impact PolyPhen http //genetics.bwh.harvard.edu/pph/ Prediction of structural and functional effects of SNPs... 

Current efforts toward oPE foldamers have focused on developing a computational model that will allow useful predictions of structure. This model was validated by comparing computational results to previously published experimental results [101]. For both crystal structure data and methyl- and hydrogen-series mPEs [25,57], the MMFF molecular mechanics system [102,103]... 

In the benzofuroxan series ab initio calculations at the MP2 level give qualitatively correct predictions of structure, whereas semiempirical AMI, PM3 treatment is less satisfactory showing a preference for the dinitroso tautomer <94jpci2933>. The most likely intermediate in the interconversion of (9a) and (9b) is considered to be anri-l,2-dinitrosobenzene which is predicted to have an energy 50 kJ mol above that of benzofuroxan itself <94JOC643i>. Other calculated properties include diagmagnetic susceptibilities and IR, UV, and PE data. 

The Hartree-Fock or self-consistent-field approximation is a simplification useful in the treatment of systems containing more than one electron. It is motivated partly by the fact that the results of Hartree-Fock calculations are the most precise that still allow the notion of an orbital, or a state of a single electron. The results of a Hartree-Fock calculation are interpretable in terms of individual probability distributions for each electron, distinguished by characteristic sizes, shapes and symmetry properties. This pictorial analysis of atomic and molecular wave functions makes possible the understanding and prediction of structures, spectra and reactivities. 

In this book we have emphasized the applications of group theory to calculations of properties of molecules, focusing on developing a working knowledge of useful tools for analysis and prediction of structures and spectra. 

A comparison of the data obtained by using McDougal and Turner s treatment of the prediction of structured flow formation in the PVP-dextran system with the ternary diffusion data in Fig. 16 indicates that their theory is not compatible with our observations 36). 

Homology modelling is not an exact technique. Especially, when the extent of sequence homology (exact matches and matches between amino acid residues of similar property, e.g. hydrophobic, polar, acidic, basic) is low, then more attention will be paid to structural rather than sequence similarities and to prediction of structure for unmatched sequences. In such cases, and always when there is no crystal structure of a member of the family to provide a template, then total reliance has to be placed on the experience of the investigator or in one of the many computer programs now available. The principal methods have been reviewed by Sternberg (1986) and Blundell et al. (1987a). 

A parallel but more historically comprehensive discussion of glass structure and composition has been given (36). Prediction of structural parameters and consequent properties from theoretical principles has increased with the advent of supercomputers. Of particular interest to glass scientists... 

Predictions of structures of more complex proteins from their amino acid sequences presents a major challenge.708 Assignment of domains within the protein is a first step.709-712 Regions of probable helix or (3-strand structure can be recognized but it is difficult to predict the exact lengths of the helices and the structures of... 

The impressive selectivity for e.g. fluoride over chloride drops from a factor of fifty in dichloromethane to zero in DMSO, and is also small in acetonitrile. Calorimetric measurements show, that the complexation is dominated by enthalpy, but influenced also by entropy disadvantage which is larger for Cl" than for F (it should be noted that several published data differ significantly, also as function of addition modes). Obviously, the prediction of structures and stabilities, but in particular of selectivities in different environment is still a demanding challenge. 

While the primary structure of proteins and nucleic acids can be experimentally determined in a straight-forward manner, their higher-order structures are much more difficult to elucidate. In general, computational methods dealing with primary structure focus on interpretation of the structure-function, as in promoter analysis. By contrast computational methods working on higher-order structure instead focus on the prediction of structural details. Further, most techniques are limited to the prediction of RNA and protein structures—sugar-, fatty-add-, and DNA-structural prediction methods are in their infancy. 

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