Similarity-based descriptors

Zdrazil, B., Kaiser, D., Kopp, S., Chiba, P., and Ecker, G.E. (2007) Similarity-based descriptors (SIBAR) as tool for QSAR-studies on P-glycoprotein inhibitors influence of the reference set. QSAR ei Combinatorial Science, 26, 669-678. 

C, E E Hodgkin and Richards W G 1993. The Utilisation of Gaussian Functions for the Rapid nation of Molecular Similarity. Journal of Chemical Information and Computer Science 32 188-192. C and I D Kuntz 1995, Investigating the Extension of Pairwise Distance Pharmacophore sures to Triplet-based Descriptors, Journal of Computer-Aided Molecular Design 9 373-379. 

Lipoxygenase AnalytiCon Discovery db, Similarity based on 2D CATS descriptors 18 hits/430 tested [68]... 

The equilibrium population is said to have a structure when a substantial fraction of the molecules adopts similar conformations. But the phrase lacking structure does not imply that individual molecules comprising the ensemble lack a conformation rather, the population is too heterogeneous to be readily characterized using a coherent, structure-based descriptor. The unfolded state resists ready characterization because it is so diverse. Typical biophysical methods report ensemble-... 

In this chapter, the genesis of SMILES-based descriptors (as well as perspectives of utilization of these characteristics for QSPR/QSAR analyses) is discussed. We concluded that in fact the SMILES-based optimal descriptors are derivatives of the graph-based optimal descriptors. In fact the SMILES-based descriptors are calculated with scheme that is similar to the well-known additive scheme (Zinkevich et al., 2004), but instead of contributions for the molecular fragments (chemical elements, different kinds of cycles, covalent bonds, etc.) contributions for the SMILES fragments (c, C, n, N, Cl, Br, =,, etc.) are using. 

Molecular similarity (similarity-based virtual screening) on the basis of one or a small set of known actives, molecules showing a high similarity concerning specific features stored in a molecular descriptor are searched for. 

HertJ, Willett P, Wilton D, etal. (2004) Topological descriptors for similarity-based virtual screening using multiple bioactive reference structures. Org. Biomol. Chem. 2 3256-3266. 

Similarity-based models Between isomeric compounds Molecular descriptor... 

Two-Dimensional Descriptors derived from two-dimensional structure representa-Similarity-Based tions of a molecule are popular in ligand-based screening owing to... 

Many different structural descriptors have been developed for similarity searching in chemical databases [4] including 2D fragment based descriptors, 3D descriptors, and descriptors that are based on the physical properties of molecules. More recently, attention has focused on diversity studies and many of the descriptors applied in similarity searching are now being applied in diversity studies. Structural descriptors are basically numerical representations of structures that allow pairwise (dis)similarities between structures to be measured through the use of similarity coefficients. Many diversity metrics have been devised that are based on calculating structural (dis)similarities, some of these are described below. 

One of the most commonly used structural descriptors in similarity and diversity studies is that of the 2D fragment bitstring where a molecule is represented by a vector of binary values that indicate the presence or absence of structural features, or fragments, within the molecule. Many different similarity measures or coefficients have been developed to quantify the degree of similarity between such vector based descriptors [5-7]. Usually, the values that can be taken by a coefficient lie in the range 0..1, or they can be normalised to be within this range. A similarity coefficient of 1 indicates that the two molecules are identical with respect to the structural descriptors and a value of 0 indicates that the two molecules are maximally different... 

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