Atom environment descriptor

Atom Environment descriptors substructure descriptors (0 fingerprints)... 

A structural feature is defined by nine numbers. The first four numbers (nl-n4) serve to identify the specific atom type, atom pair, or atom environment by means of a predefined set of properties, while the remaining five numbers (n5-n9) determine which bits of the whole key are set by the feature. Specifically, in the case of single atom descriptors, nl is 0 and n2 and n3 encode one or two properties of the atom for atom pair descriptors, nl encodes the number of bonds (topological distance) between the atoms, while nl and n3 encode the property values of the two atoms finally, for custom atom environment descriptors, nl is equal to 7, while n2 encodes the specific atom environment and n3 encodes the property of the atom in the center of that environment. The number n4 encodes the number of occurrences in the molecule of the considered feature. The number n5 is used to specify the number of bits that are set, while n6 is a flag indicating whether or not hashing is allowed the final three numbers, n7, n8, and n9 identify the bits in the structural key. 

Atom environment descriptors are calculated by a two-step procedure in the first step, the Sybyl atom types are assigned to all heavy atoms in the second step, count vectors of the atom... 

Atom environment descriptor for carbon Ci of phenol. Atoms are assigned Sybyl atom types (Cl =C.ar type). A topological distance up to four is considered. The final count vector is obtained by linking the five layers (0-4) into a unique string. 

Bender, A., Mussa, H.Y., Glen, R.C., and Reding, S. (2004) Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D) evaluation of performance. Journal of Chemical Information and Computer Sciences, 44 (5), 1708-1718. 

Figure 6.6 Examples ofthree context-sensitive the localized atom environment descriptor. The transformations. Dark gray, black, and light gray p-values signify the statistical significance of colors indicate favorable, unfavorable, and zero these observations.The numberofexamples for...

Carhart et al. [15] described a generalized structural descriptor called an atom pair which is defined in terms of the atomic environments of, and shortest path separation between, all pairs of atoms in the topological representation of a chemical structure. A similar descriptor has been suggested by Klopman [16]. More recently, Judson [20] described a more sophisticated approach to analyze structural feature of molecules for structure-activity studies. 

The path environment descriptor is similar to the molecular connectivity environment descriptor. A substructure is matched against the structure being coded. If it is present, then a pseudomolecule is formed from the substructure atoms and their first nearest neighbor atoms. Then the number of paths originating from the set of atoms forming the pseudomolecule is found. The maximum path length to be considered is input by the user. 

Table II. The substructures used for the generation of the environment descriptors and the sigma charge descriptors are shown in Figure 2. In this figure a terminal X indicates an atom of undetermined type and undetermined connectivity. An X found imbedded in a substructure, such as the X found in substructure 4 is constrained to have the connectivity found in the substructure to obtain a match, but any atom type. For example, the substituent on the benzo ring is substructure 5 can be a methyl group, a chlorine, or an ethyl group, among others. The mean and standard deviation for each descriptor and the values for 7,12-dimethyl benz(a)anthracene are shown in Table III.

Steric environment of the amine nitrogen atom The descriptors used to determine the principal properties of amines do not take steric effects into account. It is therefore suggested that steric factors should be considered as a separate additional criterion when test items are selected. 

Local, or atomic, RDF descriptors are snitable to characterize an individual atom in its chemical environment. They are nsnally not appropriate for investigations of diverse data sets, since each A-atomic molecnle can have N local descriptors. A typical application of local descriptors is the characterization of steric hindrance at reaction centers. This can be performed nsing a conseqnent numbering of the atoms of the reactants. In the following experiment, the Rnthenium atom of each conformer shown in Figure 5.8 was the first atom in the data file, and the local RDF descriptors for atom 1 (Ru) were calculated. Figures 5.10a through 5.10c show the results for the Cartesian RDF descriptors. 

Aimed at characterizing the local environment of atoms, these descriptors are calculated by applying the autocorrelation function to encode spatial information relative to each single ith atom in a molecule as [Nohair, Zakarya et al., 2002 Nohair and Zakarya, 2003]... 

Similar to —> MNA descriptors, signature descriptors are holographic vectors of count numbers of all the atomic signatures present in the data set molecules, the signature of an atom being a canonical representation of the atom environment up to a predefined depth, that is, a circular substructure descriptor [Visco, Pophale et al, 2002 Faulon, Visco et al, 2003]. 

There are several ways in which molecular descriptors can be classified. The majority of descriptors are atom-based rather than field-based. The bulk of this review is focused on a discussion of atom-based descriptors. As the name implies, atom-based descriptors are based on individual atoms, with the description extending outward to incorporate information about the atom s environment. The descriptors are typically generated by analysis of 2D or 3D connection tables, and can include ID, 2D, or 3D information about the molecule. Atom-based descriptors include individual atoms, feature counts, substructural fragments, topological indices, atomic properties, pharmacophores (see Chapters 17 and 18 of this book), and calculated physicochemical properties. 

After the MMPs and their respective contexts and transformations had been generated and stored in the database, several descriptors were employed in order to represent the context of matched molecular pairs. The approach included the consideration of both the local environment around the attachment point and whole molecule/context representations. This division allowed for a hierarchical view of the context representation, starting from the whole molecule and focusing progressively on the well-defined local area where the transformation took place. For the whole molecule representation approach, Murcko frameworks [30] were employed. For the localized approach, atom environments [31] were used. 

This parametric approach to spectral simulation was developed and utilized by Grant and Paul and Lindeman and Adams in their studies of linear and branched alkanes. These initial studies involved the calculation of simple topological parameters to be used as descriptions of the local structural environments of carbon atoms. This approach has been implemented more extensively and effectively with an interactive computer system that handles the calculation and manipulation of large numbers of structural descriptors. Topological, geometric, and electronic representations of local atomic environments can be encoded as descriptors. This computational methodology has been successfully applied to several structural classes of compounds cydo-hexanols and decanols, steroids, cyclopentanes and cyclopentanols, nor-bornanols, decalones, and carbohydrates. ... 

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