Structure Analysis and Prediction

Table 1 Online resources for protein structure analysis and prediction...

Parthiban V, Gromiha MM, Hoppe C, Schomburg D. Structural analysis and prediction of protein mutant stabihty using distance and torsion potentials role of secondary structure and solvent accessibility. FYoteins. 2007 66 41-52. 

The hope that promiscuity is predictable is also supported by the identification of systematic patterns of promiscuity. For example, lactonases, and in particular lactonases that favor hydrophobic lactones, show a consistent tendency to promiscuously catalyze the hydrolysis of phosphotriesters. This pattern has now been seen in lactonases from three different superfamilies PLLs (TIM-barrels from the amidohydrolase superfamily Table 1, entry 11) PONs, or serum paraoxonases (calcium-dependent six-bladded /3-propellers Table 1, entry 13) and AHA (a lactonase from the metallo-/3-lactamase superfamily Table 1, entry 12). That very different scaffolds and active-sites configurations share the same promiscuity pattern suggests that these reactions share a key feature, probably in the geometry of their transition states. This feature must be distinct, also because many of these lactonases do not hydrolyze esters that are much closer to lactones than phosphotriesters, and should thus be amenable to structural analysis and prediction. 

Structure Analysis and Prediction 11.1 The Global Instability Index... 

Cohen F E, M J E Sternberg and W R Taylor 1982 Analysis and Prediction of the Paclung oi. i-E a iinst a /3-Sheet in the Tertiary Structure of Globular Proteins. Journal of AdoljcuLir E 156 821-862. 

Melcher, R. E. 1987. Structural Reliability Analysis and Prediction. Halsted Press/Wiley, New York. 

BVB Reddy TL Blundell. Packing of secondary structural elements m proteins. Analysis and prediction of mter-helix distances. J Mol Biol 233 464-479, 1993. 

Analysis and prediction of side-chain conformation have long been predicated on statistical analysis of data from protein structures. Early rotamer libraries [91-93] ignored backbone conformation and instead gave the proportions of side-chain rotamers for each of the 18 amino acids with side-chain dihedral degrees of freedom. In recent years, it has become possible to take account of the effect of the backbone conformation on the distribution of side-chain rotamers [28,94-96]. McGregor et al. [94] and Schrauber et al. [97] produced rotamer libraries based on secondary structure. Dunbrack and Karplus [95] instead examined the variation in rotamer distributions as a function of the backbone dihedrals ( ) and V /, later providing conformational analysis to justify this choice [96]. Dunbrack and Cohen [28] extended the analysis of protein side-chain conformation by using Bayesian statistics to derive the full backbone-dependent rotamer libraries at all... 

Cohen, F.E., Sternberg, M.J.E., Taylor, W.R, Analysis and prediction of the packing of a-helices against a p-sheet in the tertiary structure of globular proteins. 

Other computer models and analytical tools are used to predict how materials, systems, or personnel respond when exposed to fire conditions. Hazard-specific calculations are more widely used in the petrochemical industry, particularly as they apply to structural analysis and exposures to personnel. Explosion and vapor cloud hazard modeling has been addressed in other CCPS Guidelines (CCPS, 1994). Again, levels of sophistication range from hand calculations using closed-form equations to numerical techniques. 

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. 

In this chapter we have outlined how the use of a universal thermodynamic approach can provide valuable insight into the consequences of specific kinds of biopolymer-biopolymer interactions. The advantage of the approach is that it leads to clear quantitative analysis and predictions. It allows connections to be made between the molecular scale and the macroscopic scale, explaining the contributions of the biopolymer interactions to the mechanisms of microstructure formation, as well as to the appearance of novel functionality arising from the manipulation of food colloid formulations. Of course, we must remind ourselves that, taken by itself, the thermodynamic approach cannot specify the molecular or colloidal structures in any detail, nor can it give us information about the rates of the underlying kinetic processes. 

There has been a great deal of analysis and prediction of stable spatial patterns from various model schemes other than that considered here. It is very much harder to find any experimental examples of such stable stationary structures in chemical systems. This may be because the first type considered in 10.3 (diffusion-driven instabilities) require unequal diffusivities and are particularly favoured when the ratio is very much larger than unity. With the various intermediate chemical species which are believed to participate in,... 

Theoretical investigations enable analysis and prediction of molecular properties when molecules are interacting with a structured environment. For this research area it is important to understand the relationship between the molecular structure, structured environments and molecular properties [2-4,32-44],... 

The process of careful, structured analysis and evaluation used to eliminate hazards during design and construction will also allow a chemical facility to accurately predict unplanned events that may create emergencies, and to effectively prepare to manage them should they occur. A comprehensive emergency preparedness program has all of these elements prevention, prediction, and preparation. 

We consider a reactor with a bed of solid catalyst moving in the direction opposite to the reacting fluid. The assumptions are that the reaction is irreversible and that adsorption equilibrium is maintained everywhere in the reactor. It is shown that discontinuous behavior may occur. The conditions necessary and sufficient for the development of the internal discontinuities are derived. We also develop a geometric construction useful in classification, analysis and prediction of discontinuous behavior. This construction is based on the study of the topological structure of the phase plane of the reactor and its modification, the input-output space. 

The computational studies on protein structures have been carried out from different perspectives in biology. These perspectives include 1) comparison of protein structures, 2) structural analysis, and 3) protein structure prediction. Table 1 lists the online resources that are providing such services. 

The analysis and prediction processes are separated. The analysis phase generates sets of equations for groups found to be significant to activity in a training set of chemical structures. Conventional statistical measures of validity are computed. The application supplied to an end-user applies these models to query compounds and reports the predictions derived from the equations. The user can ask for information about the statistical quality of the models and about how well the query compounds fit into the prediction space of the models. Depending on whether models have been derived from public or confidential data, the user may be able to view the structures that were used in the training set. 

Layer 3 Analysis and prediction of molecular structure (6 o clock position in Figure 1.7)... 

Although a theoretical method to predict the three-dimensional structure of a protein from its sequence alone is not in sight yet, researchers have uncovered a multitude of connections between the primary sequence on one hand and various functional features of proteins on the other hand. Among the success stories are the recognition of transmembrane proteins or the classification of proteins into classes of similar function based on sequence similarity. The latter achievement uses the observation that proteins that are similar in sequence are likely to share similar functional features. This is also giving rise to the enormous utility of similarity searches in sequence data bases. This Chapter will deal with the kinds of analysis and predictions based on primary sequence alone and the algorithms used in this field. 

Today, analysis and prediction methods have mostly a statistical flavor. They are trained on classified data and make new classifications or predictions based on statistical models. In some sense, all Chapters of Volume 1 present such methods. For instance, the methods for homology-based protein structure prediction in Chapter 5 and 6 of volume 1 learn from a set of observed structures rules that predict alike structures. 

F. E. Cohen, M. j, E. Sternberg, and W. R. Taylor, /. Mol. Biol., 156, 821 (1982). The Analysis and Prediction of the Tertiary Structure of Globular Proteins Involving the Packing of a-Helices against a P-Sheet A Combinatorial Approach. 

Nucleotide analysis and predicted amino acid sequence K. S. Cook et ah, Proc. Nat. Acad. Sci. USA 82. 6480 (1985). Structure of adipsin gone H. Y. Min, B. M. Sp/egel man. Nucleic Acids Res. 14, 8879 (1986). I so In front adipose tissue, reportedly the primary site of synthesis and from sciatic nerve K. S. Cook el ah. Science 237, 402 (1987). Studies in murine obesity model and potential biological role J, S. Flier et ah, ibid. 405. 

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