Chemoinformatics tools

The JME Editor is a Java program which allows one to draw, edit, and display molecules and reactions directly within a web page and may also be used as an application in a stand-alone mode. The editor was originally developed for use in an in-house web-based chemoinformatics system but because of many requests it was released to the public. The JME currently is probably the most popular molecule entry system written in Java. Internet sites that use the JME applet include several structure databases, property prediction services, various chemoinformatics tools (such as for generation of 3D structures or molecular orbital visualization), and interactive sites focused on chemistry education [209]. 

Goodnow, R.A., Jr, Gillespie, P., Bleicher, K. Chemoinformatic tools for library design and the hit-to-lead process a user s perspective. In Chemoinformatics in Drug Discovery, Oprea, T.I. (ed.) Wiley-VCH, Weinheim, 2004, 381-435. 

Chemoinformatic Tools for Library Design and the Hit-to-Lead Process A User s Perspective... 

Two of the other factors that are important to many chemists are patentability and the number of active compounds in the set of validated hits. Current chemoinformatics tools are not well suited to predict these factors. 

Chemoinformatic Tools and Strategies to Visualize Active Libraries... 

Deliver the most generally useful chemoinformatics tools directly to the bench scientist so that he/she can use them without requiring the intervention of a specialist. 

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. 

With product structures, many chemoinformatics tools can be applied to filter the virtual libraries and to select a few use-... 

To summarize, library design involves choices of diversity vs. similarity, product based vs. reactant based, and single objective vs. multiobjective optimizations. Chemoinformatics tools, such as various predictive models and chemoinformatics infrastructures, can be utilized to facilitate the selection process of library design. 

Since modern drug discovery is mainly a data-driven process and chemoinformatics is at the center of data integration and utilization, it is natural that majority of library design tools are chemoinformatics tools. Therefore, a deep understanding of chemoinformatics is necessary for taking full advantage of library technologies. 

II. Products Summary Daylight provides chemoinformatics tools and databases for life sciences. Daylight s product portfolio includes DayCart, THOR database, Merlin exploratory data analysis, ACD database, MedChem database, SPRESI database, WOMBAT database, World Drug Index database. 

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