In silico prediction of chemicalinduced hepatocellular. How to use e dragon to calculate molecular descriptors. There are thousands, if not tens of thousands, which have been published. The reliability of 3d molecular descriptors computed by dragonx has lately been investigated, thereby. The software currently calculates 797 descriptors 663 1d, 2d descriptors, and 4 3d descriptors and 10 types of fingerprints. Edragon can analyse max 149 molecules and max 150 atoms per molecule. Specifically it calculates almost 4000 descriptors independent of 3dimensional information such as constitutional, topological, phamacophore. Dragon is another widely used application software that is used to calculate molecular descriptors. Generating various molecular representations for chemicals, proteins, dnas, rnas and their interactions. What mole db molecular descriptors data base is for. Characterisation of gaschromatographic polysiloxane. These descriptors can be used to evaluate molecular structureactivity or structureproperty relationships, as well as for similarity analysis and highthroughput screening of molecule databases. The topological structure descriptors provided sound bases for classifying molecular structures. It can calculate numerous descriptors, and it has several interfaces, such as a gui, cli, web e dragon 23, which is based on an older free version of dragon, and knime.
For an extensive reference on molecular descriptors, cf. Molecular descriptors are widely employed to present molecular characteristics in cheminformatics. Qsar classification models for predicting the activity of. Chemdes is a free webbased platform for the calculation of molecular descriptors and fingerprints, which provides more than 3,679 molecular descriptors that are divided into 61 logical blocks. Dragon 5,200 benchmark software for calculating 0 to 3d descriptors and binary fingerprints. Molecular descriptors ochem users manual ochem docs.
Mold2, molecular descriptors from 2d structures for. Edragon is the electronic remote version of the well known software dragon, which is an application for the calculation of molecular descriptors developed. In this case, dragon will perform the calculations of those molecular descriptors which are hinvariant, i. Which software is best for calculating the molecular descriptor. Of them, the most important differences can be described as follows. In the last few years, a lot of molecular descriptors have been proposed derived from different theories and approaches. E dragon calculates dragon molecular indices pls implements original twostep descriptors selection procedure ufs produces a reduced data set that contains no redundancy and a minimal amount of multicollinearity. The mole db molecular descriptors data base is a free online database constituted of 1124 molecular descriptors calculated on 234773 molecules.
We selected variables from molecular descriptors calculated and standardized by dragon 6 for the following 3 reasons. In this paper, we evaluate 919 dragondescriptors of 6 different categories by means of clustering. Important variables were selected by multiple methods. Quantitative structureactivity relation qsar modeling is an alternative method that can assist in the selection of lead molecules by using the information from reference active and inactive compounds. Quantitative structureproperty relations qspr employing descriptors derived from the 3d molecular structure are frequently applied for property prediction in various fields of research. Edragon software virtual computational chemistry laboratory. Many dragon and padel descriptors are hard to interpret in terms of. Those include measures based on molecular descriptors, measures based on molecular fragments such as maccs and measures based on graph matching such as maximum common substructure searches 11. Master dragon right out of the box, and start experiencing big productivity gains immediately. In the next step for all 1115 compounds, molecular descriptors were calculated by dragon software 8. In addition, it provides 59 types of molecular fingerprint systems for drug molecules, including topological fingerprints, electrotopological state e. After briefly introducing some fundamental concepts of structureactivity applications e.
The cp ann model for prediction of carcinogenicity demonstrated good prediction statistics on the test set of 161 compounds with sensitivity of 75% and. Padeldescriptor was developed using the java language and consists of a library and an interface component. Dragon provides more than 1,600 molecular descriptors that are divided into 20 logical blocks. It provides almost 5,000 molecular descriptors of different types. The mole db molecular descriptors data base is dedicated to all the scientists who are interested in molecular descriptors andor apply molecular descriptors in scientific research. Dragon is an application for the calculation of molecular descriptors. The mdl and dragon software programs were applied for calculating the molecular descriptors. Since t he lat ter is freely availa ble for download and a free version of the dragon descriptors is available on line tetko et al. Moreover, even 2dautocorrelation descriptors can be calculated 97 descriptors. List of some software and webserver for computing molecular descriptors.
Use of chemoinformatics to identify molecular descriptors. Dragon can calculate 1664 molecular descriptors for any chemical structure. Pfas carbonfluorine bond descriptors this is a modified java code based on the approach in j. A rotationtranslation invariant molecular descriptor of. Dragon speech recognition software is better than ever. The software currently calculates 1875 descriptors 1444 1d, 2d descriptors and 431 3d descriptors and 12 types of fingerprints total 16092 bits. In this paper, the main characteristics of dragon software for the calculation of molecular descriptors are shortly illustrated. Virtual laboratory software computational chemistry. How to use edragon to calculate molecular descriptors. To address these issues, we propose mordred, a developed. However, users of those programs must contend with several issues, including software bugs, insufficient update frequencies, and software licensing constraints. Largescale evaluation of molecular descriptors by means of. Oct 18, 2018 molecular descriptors encode a wide variety of molecular information and have become the support of many contemporary chemoinformatic and bioinformatic applications. Dragon software software for the calculation of 1630 molecular descriptors version 5 dear colleagues, we would like to announce that the new dragon 5 version is now available.
E dragon can analyse max 149 molecules and max 150 atoms per molecule. These descriptors and fingerprints are calculated mainly using the chemistry development kit. Many dragon and padel descriptors are hard to interpret in terms of structure features. Introductionchemdesmolecular descriptors computing platform. Molecular descriptors encode a wide variety of molecular information and have become the support of many contemporary chemoinformatic and bioinformatic applications. Effect of coordinate rotation on 3d molecular descriptors. The new dragon 5 version has been improved as follows. Molecular descriptors have been explored extensively. A common classification method for descriptors can be taken from chemoinformatics textbooks and a collection of common molecular descriptors in the handbook of molecular descriptors.
From these studies, it is known that a large number of descriptors are strongly correlated and capture similar characteristics of molecules. Dragon is the most used software for molecular descriptors. The dragon software can compute thousands of such descriptors. Largescale evaluation of molecular descriptors by means. Dragon is the worldwide most used application for the calculation of molecular descriptors. After calculating molecular descriptors for all 1115 chemical structures, we must reject non informative descriptors from output of. Dragon molecular descriptors calculation dragon talete srl. The user can calculate not only the simplest atom type, functional. The calculator plugins, included in the marvin suite, are modules of chemaxons marvin and jchem cheminformatics platforms which calculate chemical properties descriptors from chemical structures. The software has several advantages over existing standalone molecular descriptor calculation software. It currently calculates 797 descriptors 663 1d, 2d descriptors, and 4 3d descriptors and 10 types of fingerprints. These descriptors can be used to evaluate molecular structureactivity or structureproperty relationships. E dragon is the electronic remote version of the well known software dragon, which is an application for the calculation of molecular descriptors developed by the milano chemometrics and qsar research group of prof.
Qsar new dragon 5 version software for molecular descriptors. Dragon calculation of molecular descriptors and fingerprints. The mold2 software was developed to enable the rapid calculation of a large and diverse set of descriptors encoding twodimensional chemical structure information. Molecular descriptors calculation dragon talete srl. Kode chm chemoinformatics consultancy and software development for industry and research. The selection of only these four types of descriptors from the. The screening of chemical libraries with traditional methods, such as highthroughput screening hts, is expensive and time consuming. Use of chemoinformatics to identify molecular descriptors of. Molecular descriptor an overview sciencedirect topics. A selection of commercial and free descriptor calculation utilities is collected under the molecular descriptor software collection or. Prediction of standard enthalpy of formation by a qspr model.
Look into any jcics issue from the 80s and you will find again a paper, or two, or more, by the usual suspects inventing another 50 new graphbased descriptors by squaring one of the parameters used in the previous publication and listing some values for saturated hydrocarbons as the only covered structure class. Structures, molecular descriptors, model development and. Recently, webbased descriptor generation tools have been proposed as well. Jun 24, 2019 software used for processing molecular descriptors dragon 32 is a calculation of molecular descriptors tool. Thesimple chi indices are described on page 85 of the handbook of molecular descriptors todeschiniand consonni 2000. Dragon is 3x faster than typing and its 99% accurate. Please visit kode website for details about the new. A software to calculate molecular descriptors and fingerprints. Only 49 descriptors showed statistically significant differences among auxins, cytokinins and gibberellins.
Topsmode 29 and dragon 32 computer softwares were employed to calculate the molecular descriptors. In the case of topsmode software, the polar surface, the dipole moment, the gasteigermarsili charges and hidrophobicity were used to weigh the bond adjacency matrix. These descriptors and fingerprints are calculated mainly using. Software used for processing molecular descriptors dragon 32 is a calculation of molecular descriptors tool. Calculating 293 chemical descriptors and 14 kinds of chemical fingerprints, 9920 protein descriptors based on protein sequences, more than 6000 dnarna descriptors from nucleotide sequences, and six types of interaction descriptors using three different combining strategies. However, many of them only have been used to explain a few prediction problems.
The calculation time for descriptors depends on many factors including the size of the dataset, the package selected, and the availability of computational resources. Various moleculardescriptorcalculation software programs have been developed. Molecular descriptors for structureactivity applications. Dragon speech recognition get more done by voice nuance. In particular, dragonx is one of the most widely used software packages for descriptor calculation. The descriptors and fingerprints are calculated using the chemistry development kit with additional descriptors and fingerprints such as atom type. Descriptors and their selection methods in qsar analysis.
Descriptor is a software for calculating molecular descriptors and fingerprints. Edragon is the electronic remote version of the well known software dragon, which is an application for the calculation of molecular descriptors developed by the milano chemometrics and qsar research group of prof. I have finished the second version with capacity to calculate 16,299 easily interpretable 1d to 3d molecular descriptors. Edragon calculates dragon molecular indices pls implements original twostep descriptors selection procedure ufs produces a reduced data set that contains no redundancy and a. A common classification method for descriptors can be taken from chemoinformatics textbooks and a collection of common molecular descriptors in the handbook. Software for the calculation of 1630 molecular descriptors. Various molecular descriptorcalculation software programs have been developed. Dragon dragon is an application for the calculation of molecular descriptors. Mopac2016derived descriptors you can select one or more descriptor packages to calculate for the same dataset. A read is counted each time someone views a publication summary such as the title, abstract, and list of authors, clicks on a figure, or views or downloads the fulltext.
Jan 15, 2014 mopac2016derived descriptors you can select one or more descriptor packages to calculate for the same dataset. Impact of molecular descriptors on computational models. An easy approach to molecular descriptor calculations. Mar 22, 2004 dragon software software for the calculation of 1630 molecular descriptors version 5 dear colleagues, we would like to announce that the new dragon 5 version is now available. Visit the products section for the list of available software.
1396 564 335 1159 263 911 968 1375 1040 1015 953 808 1216 1366 751 1202 602 1267 995 1352 844 1148 1224 598 551 1474 502 524 529 386 704 489 1601 417 253 1027 500 316 4 495 442 255 1489