Comparative molecular surface analysis

Polanski J, Gieleciak R, Bak A (2002) The comparative molecular surface analysis (COMSA) - a nongrid 3D QSAR method by a coupled neural network and PLS system Predicting pKa values for benzoic and alkanoic acids. J Chem Inf Comput Sci 42 184-191... 

Comparative Molecular Similarity Indices Analysis grid-based QSAR techniques > Comparative Molecular Surface Analysis grid-based QSAR techniques > Comparative Receptor Surface Analysis = CoRSA > Comparative Spectral Analysis spectra descriptors... 

COMSA = Comparative Molecular Surface Analysis topological feature maps... 

Self-organizing map for describing chemical information of a molecule is also used in —> Comparative Molecular Surface Analysis and topological feature maps. 

Several QSAR approaches are based on Kohonen maps, such as topological feature maps. Comparative Molecular Surface Analysis, and MOLMAP descriptors. Counter-propagation neural network is a development of Kohonen maps for classification purposes [Zupan, Novic et al., 1995], which considers a set of output layers, called Grosberg... 

The Comparative Molecular Surface Analysis (CoMSA) is a 3D-QSAR approach that makes use of the topological feature maps combined with PLS method to quantitatively predict... 

Hasegawa, K., Morikami, K., Shiratori, Y, Ohtsuka, T, Aoki, Y. and Shimma, N. (2003) 3D-QSAR study of antifungal N-myristoyltransferase inhibitors by comparative molecular surface analysis. Chemom. Intell. Lab. Syst., 69, 51—59. 

Polanski, J. and Gieleciak, R. (2003) The comparative molecular surface analysis (CoMSA) withmodified uniformative variable elimination-PLS (UVE-PLS) method application to the steroids binding the aromatase enzyme. J. Chem. Inf. Comput. Sci., 43, 656—666. 

Polanski, J. and Walczak, B. (2000) The comparative molecular surface analysis (COMSA) a novel tool for molecular design. Computers Chem., 24, 615-625. 

Further additions to the 3D-QSAR arsenal include comparative molecular similarity indices analysis (CoMSIA) [15], 4D-QSAR [16], COMPASS [17], receptor surface models [18], the pseudoreceptor approach [19], ComPharm [20], and comparative molecular surface analysis (CoMSA) [21], 3-D-invariant, alignment-free descriptor systems such as comparative molecular moment analysis (CoMMA) [22], EVA [23], WHIM [24], and ALMOND [25], have also become available. A survey of the 3D-QSAR literature reveals 1154 entries in the Chemical Abstracts Plus database of these, 79% are journal publications, 19% are conference proceedings, and four are patents related to, or using, 3D-QSAR models. As the number of potential targets amenable to drug discovery is increasing exponentially, it is likely that 3D-QSAR models and methodologies will continue to be developed in the next decade. 

USE 3D QSAR study of hypolipidemic asarones by comparative molecular surface analysis [7519]. 

Hahn M, Rogers D (1998) Receptor surface models. In Kubinyi H, Folkers G, Martin YC (eds) 3D QSAR in drug design, vol. 3 Recent Advances. Kluwer, Dordrecht, pp 117-133 Haji-Momenian S, Rieger JM, Macdonald TL, Brown ML (2003) Comparative molecular field analysis and QSAR on substrate binding to cytochrome P450 2D6. Bioorg Med Chem 11 5545-5554... 

Besides comparing how well a family of molecules overlaps with a reference molecule, there are sophisticated software packages that determine the phy.sictxrhcmical parameters located at specific distances from the surface of the molecule. An c.xample of this approach is comparative molecular field analysis (CoMFA). This technique is described ill more detail in Chapter. T. 

Molecular Moment Analysis, Comparative Receptor Surface Analysis, and topological feature maps. 

The mapping of properties to surface features in SPERM can be regarded as a limiting case of the last class of local similarity measures to be discussed here, these being measures that are based upon electrostatic, steric, and hydrophobic fields analogous to those that underlie current approaches to 3D QSAR (see Comparative Molecular Field Analysis (CoMFA) and Quantitative Structure-Activity Relationships in Drug Design). 

Ligand structures can be represented by molecular fields (electrostatic or steric), which contain enthalpic contributions to binding when implemented by conventional comparative molecular field analysis (CoMFA) (see Comparative Molecular Field Analysis (CoMFA)). Steric volume incorporated in molecular shape analysis (MSA) (Figure la) is another representation commonly used in SAR studies (see Molecular Surface and Volume) Alternatively, in the hypothetical active site lattice (HASL) approach, molecules are represented by a three-dimensional grid of points (lattice) associated with discrete electronic properties. ... 

Molecular Probe Analysis. In an effort to understand how a molecule is seen by either another molecule or by a surface, molecular probes can be moved around a chemical to map out its surface. These probes include anions and cations (point charges) and hard spheres or can be constructed as a combination of these. The empirical potential energy is computed at a variety of points around the test molecule and an energy surface is thus generated. This can be examined graphically and compared as changes are made to the molecule. 

On the other hand, there is considerable interest to quantify the similarities between different molecules, in particular, in pharmacology [7], For instance, the search for a new drug may include a comparative analysis of an active molecule with a large molecular library by using combinatorial chemistry. A computational comparison based on the similarity of empirical data (structural parameters, molecular surfaces, thermodynamical data, etc.) is often used as a prescreening. Because the DFT reactivity descriptors measure intrinsic properties of a molecular moiety, they are in fact chemical fingerprints of molecules. These descriptors establish a useful scale of similarity between the members of a large molecular family (see in particular Chapter 15) [18-21],... 

Ekins et al. (163) used the rat ortholog 2B6 to generate a pharmacophore model and compared these findings with a partial least squares (PLS) model using MS-WHIM descriptors. The model was constructed using 16 B-lymphoblastoids and yielded a good cross-validated r2 of 0.607. The analysis included molecular surface properties (size) together with positive elec-... 

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