Functional prediction

L Rychlewski, B Zhang, A Godzik. Fold and function predictions for Mycoplasma genitalmm proteins. Fold Des 3 229-238, 1998. 

For the Cs and K substituents, all three DFT functionals produce similar structures. All three functionals predict frequencies which are somewhat lower than the observed values but which reproduce the trends in the experimental data quite well. The SVWN5 frequencies tend to be higher than those computed by BLYP and B3LYP. 

Raha K, Merz KM. Large-scale validation of a quantum mechanics based scoring function predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes. J Med Chem 2005 48 4558-75. 

Onsager and Machlup [32] gave an expression for the probability of a path of a macrostate, p[x]. The exponent may be maximized with respect to the path for fixed end points, and what remains is conceptually equivalent to the constrained second entropy used here, although it differs in mathematical detail. The Onsager-Machlup functional predicts a most likely terminal velocity that is exponentially decaying [6, 42] ... 

Function prediction Predict the function of unknown genes based on the similarity of their gene expression profiles to those of known genes These experiments require a large database of known expression profiles that can be used for comparisons. This approach will become powerful as such databases continue to grow over the next several years. 

Why—and when—does the Fukui function work The first restriction—already noted in the original 1984 paper—is that the Fukui function predicts favorable interactions between molecules that are far apart. This can be understood because when one uses the perturbation expansion about the separated reagent limit to approximate the interaction energy between reagents, one of the terms that arises is the Coulomb interaction between the Fukui functions of the electron-donor and the electron-acceptor [59,60],... 

Smith, 1992). All of these can identify an optimal alignment between the query and either a set of previously studied sequences or a pattern of sequence elements identified as common to a set of previously studied proteins. De novo sequence analysis methods have proved less useful. Although there has been some slow progress in predicting a protein s structure from its sequence, no direct functional predictions methods have been developed. 

A major problem in function prediction is the multidomain nature of many proteins, where a protein can be assigned die function of another, even though it may only share a single common domain. Such... 

Pawlowski, K, Zhang, B., Rychlewski, L., and Godzik, A. (1999). The Helicobacter pylori genome from sequence analysis to structural and functional predictions. Proteins 36, 20-30. 

III. Gene and Function Prediction by Conservation of Genomic Context. 357... 

Fig. 7. Orthology and function prediction using synteny. A neighbor joining clustering...

Ponting, C. P., Proteins of the endoplasmic-reticulum-associated degradation pathway domain detection and function prediction, Biochem. J., 2000, 351 Pt 2, 527. 

The results obtained from the experimental studies confirm that the information-processing functions predicted by the pertinent analytical models can be achieved experimentally. Moreover, these results support the view that artificial biochemical neurons can be implemented in practice for informationprocessing purposes. Furthermore, because of the very high dependence of the system function on the internal parameters and the relations between them, the analytical models developed are essential tools for the engineering design of such systems as well as for determination of the operational parameters required for these systems to perform the information-processing function desired. 

Just as thermodynamic methods provide only a limiting value for the yield of a chemical reaction, so also do they provide only a limiting value for the work obtainable from a chemical or physical transformation. Thermodynamic functions predict the work that may be obtained if the reaction is carried out with infinite slowness, in a so-called reversible manner. However, it is impossible to specify the actual work obtained in a real or natural process in which the time interval is finite. We can state, nevertheless, that the real work will be less than the work obtainable in a reversible situation. 

Soon thereafter, chirality was recognized as a necessary and indispensible part of synthetic receptor molecule design and function. Predictably, not only has nature s chiral pool been called upon to supply inexpensive and readily available sources of chirality, but the ability of the chemist to resolve optically active precursors from racemic modifications prepared in the laboratory has been exploited ingeniously in a number of different directions. The various elements of chirality centers, axes, planes, as well as helices, have been incorporated into both axially symmetric and asymmetric receptors. 

Skolnick J, BryKnski M (2009) FINDSITE a combined evolution/structure-based approach to protein function prediction. Brief Bioinform 10 378-391... 

For Kosan and others in the pharmaceutical industry, the intent is to learn enough about these enzymes from a structure-function viewpoint so they can be manipulated. Because polyketides are built by starting from one point and continuing sequentially along the pathway dictated by protein structure, a biochemist can trace through a molecule and make structure-function predictions for the assembly enzymes with reasonable accuracy. Using recombinant DNA methods,... 

An early application of the jellium model is to estimate the work function (Bardeen, 1936 Smith, 1968). In the jellium model, there is only one parameter G. The work function is then a function of r, only. In reality, the work function depends not only on the material, but also on the crystallographic orientation of the surface. For most metals used in STM, the work function predicted by the jellium model is 1-2 eV smaller than the experimentally observed values, as shown in Table 4.1. 

As shown, the jellium model gives inaccurate predictions for the work functions. The work functions predicted by first-principles calculations (see Section 4.7) are much more accurate. 

Canales, J.J. and Graybiel, A.M. (2000) A measure of striatal function predicts motor stereotypy. Nat Neurosci 3 377-383. 

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