Property descriptors

Raevsky, 0. A., Grigor ev, V. Ju., Raevskaja, 0. E., Schaper, K.-J. Physicochemical properties/descriptors governing the solubility and partitioning in water-solvent-gas systems. Part 1. Partitioning between octanol and air. 

After all the careful filtering, there was neither a single molecular property from the profiles discussed above which could effectively discriminate the two classes nor a predictive model obtained from all those property descriptors. Only after... 

Kearsley, S.K., Saliamack, S., Eluder, E.M., Andose, J.D., Mosley, R.T., and Sheridan, R.P. Chemical similarity using physiochemical property descriptors. 

Recently, Jung et al. [42] developed two artificial neural network models to discriminate intestinal barrier-permeable heptapeptides identified by the peroral phage display experiments from randomly generated heptapeptides. There are two kinds of descriptors one is binary code of amino acid types (each position used 20 bits) and the other, which is called VHSE, is a property descriptor that characterizes the hydrophobic, steric, and electronic properties of 20 coded amino acids. Both types of descriptors produced statistically significant models and the predictive accuracy was about 70%. 

In contrast to partitioning methods that involve dimension reduction of chemical reference spaces, MP is best understood as a direct space method. However, -dimensional descriptor space is simplified here by transforming property descriptors with continuous or discrete value ranges into a binary classification scheme. Essentially, this binary space transformation assigns less complex -dimensional vectors to test molecules, with each dimension having unity length of either 0 or 1. Thus, although MP analysis proceeds in -dimensional descriptor space, its dimensions are scaled and its complexity is reduced. 

Breneman, C. M. and Rhem, M. (1997) QSPR Analysis of HPLC column capacity factors for a set of high-energy materials using electronic van der Waals surface property descriptors computed by transferable atom equivalent method. J. Comput. Chem. 18, 182-197. 

P. (1996) Chemical similarity using physio-chemical property descriptors. J Chem Inf Comput Sci 36, 118-127. 

A QSAR seeks to relate quantitative properties (descriptors) of a compound with other properties such as drug-like activity or toxicity. The essential assumption of QSAR is that quantities that can be conveniently measured or calculated for a compound can be used to accurately predict another property of interest (e.g., antibacterial activity) in a nontrivial way. QSAR has become an integral part of screening programs in pharmaceutical drug-discovery pipelines of small compounds and more recently in toxicological studies (69). However, the use of QSAR modeling applied to the search for antimicrobial peptides is relatively recent. Advances in this area are reviewed in brief here. 

However, in the first instance, QSAR attempts to express compound potency as a linear function of various structural and property descriptors D with coefficients weighting their relative importance ... 

MDL QSAR MDL Information Systems, Inc. www.mdl.com/products/predictive/qsar/index.jsp Molecular property descriptors, total topological descriptors, E-state indices... 

Kearsley SK, Sallamack S, Fluder EM, Andose JD, Mosley RT, Sheridan RP, Chemical similarity using physiochemical property descriptors, J. Chem. Inf. Comput. Sci., 36 118-127, 1996. 

Chemometrics can be employed to develop a mathematical relationship between chemical property descriptors (e.g. bond lengths, polarity, steric properties, reactivities, functionalities) and biological functions, via a computational model such as principal components analysis. The question asked is whether it is really necessary to test all... 

Principal component analysis of property descriptors of classes of compounds reveals the principal properties. The variation of the principal properties between the compunds is measured by the scores. This variation is displayed by the score... 

A set of 28 Lewis acids were characterized by ten property descriptors compiled from the literature. The data are shown in Table 9. 

Table 9. Lewis acids characterized by ten property descriptors...

The first example of principal properties for synthetic experiments was PC analysis of a set of 82 solvents, characterized by eight property descriptors [55]. The analysis was carried out with a view to finding rational principles for selecting test solvents for new reactions. Principal properties of solvents have now been determined from an augmented data set of 103 solvents characterized by nine descriptors [56]. A score plot is shown in Sect. 5.3.2 in the example on the Fischer indole synthesis. 

A set of 126 primary, secondary, and tertiary amines characterized by seven property descriptors afforded two significant principal components which described 85% of the total variance. For details, see [63]. A preliminary study of 29 amines was used for the selection of co-substrates in studies on the Willgerodt-Kindler reaction [21]. 

Empirical, semiempirical, and ab initio methods have been used extensively to calculate molecular descriptors. These molecular property descriptors help capture important characteristics of compounds such as bioavailability and receptor affinity. Descriptors such as octanol-water partition coefficient (log P), HOMO/LUMO energies, hammett a, total energy, heats of formation, ionization potential, atomic charges, electron densities, dipole/quadrupole moments, volume, and polar surface area are common examples. For an excellent review of physicochemical descriptors, the reader is directed to the following reference. ... 

Contrera, J.F., Matthews, E.J., Kruhlak, N.L., Benz, R.D. (2008). In silico screening of chemicals for genetic toxicity using MDL-QSAR, nonparametric discriminant analysis, e-state, connectivity, and molecular property descriptors. Toxicol. Mech. Meth. 18 207-16. 

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