QSAR world

QSAR World, http //www.qsarworld.com/ (accessed April 18,2008). 

There are many sources of sample structure files. The examples used in this book come from the pubchem project8 and the QSAR world project.9 There are SMILES files available from the National Cancer Institute of the National Institutes of Health.10... 

W. A. Warr, QSAR World, 2008, http www.qsarworld.com INCHIl. php. 

Another problem with the choice of descriptors is accessibility. Some types of proprietary parameters are only available through the licensing of commercial software. There are, however, some web-based resources, such as Chembench (http //chembench.mml.unc.edu) and the Virtual Computational Chemistry Laboratory (www.vcclab.org) which both provide not only descriptor calculation facilities, but also access to statistical analysis routines. The molecular descriptors website (www.moleculardescriptors.eu) and QSAR world websites (www.qsarworld.com/qsar-web-based-programs.php) also provide useful links to resources such as databases and programs. 

This is already the 37th volume in our series on Methods and Principles in Medicinal Chemistry which started in 1993 with a volume on QSAR Hansch Analysis and Related Approaches, written by Hugo Kubinyi. An average release of roughly three volumes per year indicates the increasing appreciation of the series in the MedChem world. 1 want to express my sincere thanks to my editor friends Hugo Kubinyi and Gerd Folkers for their continuous and precious contributions to the steady development of our series. 

Labute, P. (1999) Binary QSAR a new method for quantitative structure activity relationships. Proceedings of the 1999 Pacific Symposium, World Scientific Publishing, Singapore. 

So many calculation methods have been published in the last five years that it is not possible to examine them all in detail in this chapter, which does discuss the strengths and weaknesses of the various approaches. For convenience and reproducibility, most users require computerized calculation, and so this chapter emphasizes these methods. Man-nhold (1996) recently published a comparative study and van de Waterbeemed (1996) published a list of addresses for the programs. More information is available on the World Wide Web (http / / www.pharma.ethz.ch/qsar/logp.html). 

Another important consideration in the selection of a test set is to ensure that the chemicals in the data set relate to the real problem in question. It should be emphasized that the QSAR models developed in our project are used primarily to predict the activity of environmental chemicals, mostly pesticides and industrial chemicals. A data set reported by Nishihara et al. (Nishihara et al., 2000) was also selected as a test set. This data set contains 517 chemicals tested with the yeast two-hybrid assay, of which over 86% are pesticides and industrial chemicals. Only 463 chemicals were used for this validation study after structure processing. Only 62 chemicals were categorized as active on the basis of having on activity greater than 10% of 10 7M H2, as defined in the original paper (Nishihara et al., 2000). The majority of the chemicals were inactive, which is similar to the real-world situation where inactive chemicals are expected from a large proportion of those in the environment. 

I was a young organic chemist when I met Prof. Sergio Clementi, but from the very first moment I understood that his guide to the world of Chemometrics would have been a brainwashing for me. And indeed it was so. Sergio was a splendid teacher and what I know in the field of QSAR and Chemometrics is totally due to him. 

Labute P. Binary QSAR A new method for the determination of quantitative structure-activity relationships. In Altman RB, Dunker AK, Hunter L, Klein TE, Lauderdale K, editors, Proceedings of the Pacific Symposium on Biocomputing 99. River Edge, NJ World Scientific, p. 444-55. 

Hansch QSAR and related approaches belong to the world of numbers conceptually, knowledge-based expert system approaches do not. Three areas of debate about expert systems have arisen from the distinction. Can you devise ways to generate qualified output from computer-based expert systems without hiding quantitative methods inside them Assuming you can, how do you validate an expert system How can you usefully combine output from different systems—some quantitative and some qualitative—to make predictions more reliable The first of the questions is more a historical than a current one some of the systems described earlier in this chapter demonstrate... 

Erd, P. (1998a) QSAR analysis through the World Wide Web. Chimia, 52, 673-677. 

Labute, P. (1999) Binary QSAR a new method for the determination of quantitative structure-activity relationships, in Pacific Symposium on Biocomputing 1999, Vol. 7 (eds R.B. Altman, A.K. Dunker, L. Hunter, T.E. Klein and K. Lauderdale), World Scientific, NJ, pp. 444—455. 

The considerable lack of experimental data for the fate and effects assessment of environmental contaminants requires the provisional use of substitutes. For this purpose, QSAR estimates are superior to the alternative of using uniform default values, which do not allow differentiation and ranking of the potential hazards of diverse chemicals. QSAR data-quality requirements for assessing environmental hazards and risks have to be evaluated relative to the quality of the available experimental data and the relevance of the accuracy of the individual data for subsequent hazard and risk classifications. Within these assessment schemes, several factors are usually ignored for the sake of scientific precision and standardization. The simplifications of the real world apply, regardless of whether experimental or calculated input data are used ... 

The pharmaceutical world likes to use QSAR techniques for predicting just about any effect of interest. The approach has many merits, but generalizations from different QSAR analyses of ostensibly the same topic are hard to come by because different QS ARs tend to use different parameters for their best fit. 

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