DRAGON software

Dragon Software for calculation of molecular descriptors, by Todeschini R., Consonni V., Mauri A., Pavan M. Talete srl, www.talete.mi.it, Milan, Italy, 2004. 

We use assay data from a National Cancer Institute HIV/AIDS database in our study (http //dtp,nci,nih.gov/docs/aids/aids data.html). As descriptors, we apply a set of six BCUT descriptors and a set of 46 constitutional descriptors computed by the Dragon software. These descriptors could be computed for 29,374 of the compounds in the database. The assay classifies each compound as confirmed inactive (Cl), moderately active (CM), or confirmed active (CA). We treat the data as a binary classification problem with two classes inactive (Cl) and active (CM or CA). According to this classification, 542 (about 1.8%) of the compounds are active. 

In addition to the physicochemical domain, the topological features of selected HIV-1 RT inhibitors, 2-(2,6-dihalophenyl)-3-(substituted pyridin-2-yl)-thiazolidin-4-ones (Fig. 26, Table 16), have been analyzed [182] with the empirical, constitutional, and graph theoretical descriptors from the DRAGON software package [47]. This study has resulted in the identification of several influential descriptors to model the inhibitory activity and the equations shown below represent some models stemming from these descriptors. 

Todeschini R, Consonni V, Mauri A, Pavan M (2003) DRAGON software version 3.0. http //disat.unimib.it/chm/Dragon.htm... 

Todeschini R, Consonni V, Pavan M. DRAGON. Software for the calculation of molecular descriptors, Version 3.0. 

DRAGON software was conceived for the calculation of molecular descriptors by Milano Chemometrics and QSAR Research Group of Todeschini. DRAGON dates back to 1996, with the name of WHIM-3D/QSAR, while the first DRAGON version was released in 2000. Some details about DRAGON are given in Refs [Tetko, 2003 Mauri, Consonni et al, 2006]. 

DRAGON descriptors are distinguished into 22 categories, which are listed in Table D8. Table D8 List of descriptor categories in DRAGON software. 

DRAGON (Software for molecular descriptor calculations), Ver. 5.5, Talete s.r.l., via V.Pisani, 13, 20124 Milano, Italy, http //www.talete.mi.it/ dragon.htm. 

Mauri, A., Consonrii, V., Pavan, M. andTodeschini, R. (2006) DRAGON software an easy approach to molecular descriptor calculations. MATCH Commun. Math. Comput. Chem., 56, 237—248. Maw, H.H. and HaU, L.H. (2000) f-state modeling of dopamine transporter binding. Validation of the model for a small data set. J. Chem. Inf. Comput. Sci., 40, 1270-1275. 

Dragon Software v. 3.0. Milano Chemometrics and QSAR Research Group, www.disat.un-... 

Todeschini, R. Consonni, V. and Pavan, M. (2001). DRAGON-Software for the Calculation of Molecular Descriptors. Release 1.12 for Windows. Available http //www.disat.unimib/chm... 

A set of n = 209 polycyclic aromatic compounds (PAC) was used in this example. The chemical structures have been drawn manually by a structure editor software approximate 3D-structures including all H-atoms have been made by software Corina (Corina 2004), and software Dragon, version 5.3 (Dragon 2004), has been applied to compute 1630 molecular descriptors. These descriptors cover a great diversity of chemical structures and therefore many descriptors are irrelevant for a selected class of compounds as the PACs in this example. By a simple variable selection, descriptors which are constant or almost constant (all but a maximum of five values constant), and descriptors with a correlation coefficient >0.95 to another descriptor have been eliminated. The resulting m = 467 descriptors have been used as x-variables. The y-variable to be modeled is the Lee retention index (Lee et al. 1979) which is based on the reference values 200, 300, 400, and 500 for the compounds naphthalene, phenanthrene, chrysene, and picene, respectively. 

Late 1990s User-friendly software to calculate large numbers of molecular descriptors from 2D structure becomes widely available both commercially and from the Internet (e.g. DRAGON)... 

I would like to thank ScanSoft Inc. for its Dragon Natu-rallySpeaking voice dictation software. I have done most of my writing in the past several years using ScanSoft s software. Its best product yet, Dragon NaturallySpeaking 7, arrived just in time to enable me to double my productivity on this book. 

A disadvantage of the majority of these software is that they do not have the capability to calculate molecular descriptors. Thus additional software, such as DRAGON [71], Molconn-Z [72], or MODEL [73], are needed to enable toxicological QSAR models to be built. 

These are various molecular descriptors ranging from count descriptors to more complex geometrical descriptors calculated by the software DRAGON [DRAGON - Talete s.r.l., 2007]. 

Calculation of ALOGP is provided by a number of software programs, such as DRAGON, MOLCAD, PROLOGP, and TSAR. 

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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