Cheminformatics software

All the calculations described in this work were performed with the use of the ChemoSoft cheminformatics software system (Ghemical Diversity Labs, Inc.). 

A special attention is given to stereochemistry, as some compounds are published without proper chirality representation even though the information is available, for example, for natural compounds and their derivatives. Furthermore, as illustrated in Fig. 13.2-8, compounds published in medicinal chemistry literature are often depicted in a human-readable format that is, structures are drawn in a format that chemists can interpret to reconstruct proper chirality. However, this format is not machine-readable , that is, cheminformatics software for 3D structural conversion, or for automatically generating IUPAC (International Union of Pure and Applied Chemistry) nomenclature, cannot perceive the stereo centers correctly... 

Chemoinformatics (or cheminformatics) deals with the storage, retrieval, and analysis of chemical and biological data. Specifically, it involves the development and application of software systems for the management of combinatorial chemical projects, rational design of chemical libraries, and analysis of the obtained chemical and biological data. The major research topics of chemoinformatics involve QSAR and diversity analysis. The researchers should address several important issues. First, chemical structures should be characterized by calculable molecular descriptors that provide quantitative representation of chemical structures. Second, special measures should be developed on the basis of these descriptors in order to quantify structural similarities between pairs of molecules. Finally, adequate computational methods should be established for the efficient sampling of the huge combinatorial structural space of chemical libraries. 

ISIS host from Symyx http //www.symyx. com/products/software / cheminformatics / isis-host/index.jsp... 

Profile CCG develops and markets scientific software for protein modeling, 3D bioinformatics, cheminformatics, molecular modeling, combinatorial chemistry, and high-throughput screening. 

Cheminformatics.org. URL http //cheminformatics.org/. Links to tools, software, events, and QSAR data sets. 

Expert systems have now been in nse for more than 40 years and have spread into nearly all imaginable areas of application. Evolving from the research area of artih-cial intelligence (Al), they can be fonnd today in commercial applications throughout the entire scientihc and technical areas. We have seen that this technology is not just stand-alone software but is supported by many technologies from mathematics, cheminformatics, bioinformatics, Al, and related areas. 

In particnlar, cheminformatics has gained increasing awareness in a wide scientific commnnity in recent decades. One of the fnndamental research tasks in this area is the development and investigation of molecnlar descriptors, which represent a molecule and its properties as a mathematical vector. These vectors can be processed and analyzed with mathematical methods, allowing extensive amounts of molecular information to be processed in compnter software. 

Landrum, G. 2006. RDKit Cheminformatics and Machine Learning Software, http //rdkit.sourceforge.net/ (accessed April 22, 2008). 

Accelrys formerly the Oxford Molecular Group. Has a Cheminformatics database that specializes in multiple suppher databases, plus a variety of software tools for chemists. http -llwww.accelrys.comlchem... 

Liu K, Feng J, Young SS (2005) A software environment for moleeular viewing, descriptor generation, data analysis and hit evaluation. J Chem Inf Model 45(2) 515-522 http //www.ehemaxon.eom/marvin/help/calculations/calculator-plugins.html http //cheminformatics.org/datasets/... 

Open Eye Inc., Cheminformatics and Molecular Modelling OpenEye Scientific Software [Online], Available at www. eyesopen.com/ (accessed 26 June 2014). 

Selecting relevant input parameters is both important and difficult for any machine learning method. For example, in QSAR, one can compute thousands of structural descriptors with software like CODESSA or Dragon, or with various molecular field methods. Many procedures have been developed in QSAR to identify a set of structural descriptors that retain the important characteristics of the chemical compounds. " These methods can be extended to SVM models. Another source of inspiration is represented by the algorithms proposed in the machine learning literature, which can be readily applied to cheminformatics problems. We present here several literature pointers for algorithms on descriptor selection. 

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