Similarity searching field-based

Moffat, K., Gillet, V. J., Whittle, M., Bravi, G., Leach, A. R. (2008) A comparison of field-based similarity searching methods Cat-Shape, FBSS, and ROCS. J Chem Inf Model 48, 719-729. 

Tbrner, D.B., Willett, R, Ferguson, A.M. and Heritage, T.W. (1995). Similarity Searching in Files of Three-Dimensional Structures Evaluation of Similarity Coefficients and Standardization Methods for Field-Based Similarity Searching. SAR QSAR EnvironRes., 3,101-130. 

Heritage, TW (1995) Similarity searching in files of three-dimensional structures evaluation of similarity coefficients and standardization methods for field-based similarity searching. SAR el QSAR Environ. Res., 3, 101-130. 

Schuffenhauer et al. [21] reported a comparative study ofbioisosteric replacements with UNITY 2D fingerprints and FBSS (field-based similarity search) using the Bioster database [22] as a source ofbioisosteric pairs. The authors report that both these 2D and 3D methods provide complementary results that were demonstrated to work synergistically when combined using data fusion. The UNITY fingerprint was reported to be very sensitive to heteroatom replacement. This sensitivity can be overcome somewhat by abstracting the atoms present in a structure into pharmacophoric features. 

D similarity search methods are quite well developed. Thus, methods which attempt to find overlapping parts (atoms and functional groups) of the molecular moieties studied were reported first [31]. As discussed above for the case of 2D searching, these methods are of combinatorial complexity. To reduce this complexity some field-based methods have been introduced. In this case, the overlap of the fields of two structures is considered as a similarity measure. 

So far, Santos has been able to express the relation between a set of coefficients af, aj J 6 / describing a vector field and the overall curvature of the stream lines of this vector field. Based on the curvature field, they constructed the measure E of the curvature distribution in the simulation box. Provided that the homogeneous curvature field of curvature c0 is the one that minimizes E, the problem of packing has been recast as a minimization problem. However, the lack of information about the gradient of the error function to be minimized does not facilitate the search. Fortunately, appropriate computer simulation schemes for similar minimization problems have been proposed in the literature [105-109]. 

Free patent information is provided by the website http //www.freepatentsonline.com/, covering U.S., EP, and PCT patents/applications and Japanese patent abstracts. In addition to the usual text-based searches in various search fields, this site also enables graphically input chemical structure searches to be performed on over 9 million compounds (including prophetic compounds) using exact structure, substructure, or chemical similarity searches. Chemistry searches using SMILES strings or chemical names are also possible. Full patent documents may be viewed in text or PDF format. 

An increasing interest of the scientific community in recent years has been shown in the fields of combinatorial chemistry, high-throughput screening, - substructural analysis, and -+ similarity searching, for which several similarity/diversity approaches have been proposed mainly based on - substructure descriptors such as -> molecular fingerprints, which are particularly suitable for informatic treatment. 

Although a theoretical method to predict the three-dimensional structure of a protein from its sequence alone is not in sight yet, researchers have uncovered a multitude of connections between the primary sequence on one hand and various functional features of proteins on the other hand. Among the success stories are the recognition of transmembrane proteins or the classification of proteins into classes of similar function based on sequence similarity. The latter achievement uses the observation that proteins that are similar in sequence are likely to share similar functional features. This is also giving rise to the enormous utility of similarity searches in sequence data bases. This Chapter will deal with the kinds of analysis and predictions based on primary sequence alone and the algorithms used in this field. 

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