Chemoinformatics virtual screening

Rarey M, Lemmen C, Matter H. Algorithmic engines in virtual screening. In Oprea TI, editor, Chemoinformatics in drug discovery (Vol. 23 of Mannhold R, Kubinyi H, Folkers G, editors. Methods and Principles in Medicinal Chemistry). Weinheim Wiley-VCH, 2005. p. 59-115. 

Rarey, M., Lemmen, C., and Matter, H. Algorithmic engines in virtual screening. In Chemoinformatics in Drug Discovery, Oprea, T.l. (Ed.). Wiley-VCH, Weinheim, 2004, 59-115. 

The SOSA approach can be enhanced by virtual screening methods which use reference compound sets and molecular descriptors together with advanced chemoinformatics methods to compare and rank the similarity of considered candidate molecules. 

The group of Prof Peter Willett from the University of Sheffield summarizes in Chapter 6 new chemoinformatics methods for similarity-based virtual screening which based on known active compounds are useful for the identification of new ligands for targets related by conserved molecular recognition. 

Xue, L. and Bajorath, J. (2000) Molecular descriptors in chemoinformatics, computational combinatorial chemistry, and virtual screening. Combin. Chem. High Throughput Screen. 3, 363-372. 

Key words Chemoinformatics, QSAR, QSPR, similarity, diversity, library design, chemical representation, chemical space, virtual screening, multiobjective optimization. 

In this chapter, we will give a brief introduction to the basic concepts of chemoinformatics and their relevance to chemical library design. In Section 2, we will describe chemical representation, molecular data, and molecular data mining in computer we will introduce some of the chemoinformatics concepts such as molecular descriptors, chemical space, dimension reduction, similarity and diversity and we will review the most useful methods and applications of chemoinformatics, the quantitative structure-activity relationship (QSAR), the quantitative structure-property relationship (QSPR), multiobjective optimization, and virtual screening. In Section 3, we will outline some of the elements of library design and connect chemoinformatics tools, such as molecular similarity, molecular diversity, and multiple objective optimizations, with designing optimal libraries. Finally, we will put library design into perspective in Section 4. 

Chemoinformatics Approaches to Virtual Screening Edited by Alexandre Varnek and Alex Tropsha Royal Society of Chemistry, 2008 Published by the Royal Society of Chemistry, www.rsc.org... 

Here we discuss the use of chemoinformatics as a powerful virtual screening methodology that presents both an alternative as well as complement to traditional structure-based docking and scoring approaches. The first published definition of chem[o]informatics defined it as ... 

Chemical library design has always been an important component of chemoinformatics studies and it could be viewed in fact a special case of virtual screening. Chapter 9 by W. Zheng and S.R. Johnson provides an expert overview of computational approaches that are employed in the design of targeted and diverse chemical libraries, including the use of property i.e., ADMET) filters. 

ZINC (Irwin and Shoichet, 2005) is a freely accessible database of increasing use in virtual screening and other computational applications. ZINC contains over 8 million purchasable compounds and it is a very attractive source of compounds to perform chemoinformatic comparisons with other collections. 

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