Free or lowpriced so that it is easy to purchase it. Edragon software virtual computational chemistry laboratory. Padeldescriptor is a software for calculating molecular descriptors and. Molecular alignments and conformational analyses of a congeneric series are explored to assess the impact of ligand substituents. Cbddgroupcomputational biology and drug design group.
Molecular descriptors calculation dragon talete srl. You need a descriptor package for descriptor calculation. Since the calculation of such quantitative representations of molecules may require substantial computational skills and efforts, several tools have been previously developed to make an attempt to ease. 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. The software currently calculates 1875 descriptors 1444 1d, 2d descriptors and 431 3d descriptors and 12 types of fingerprints total 16092 bits. Test is released by the united states environmental protection agency us epa and it is one of the qsar tools suggested as an alternative approach for the reach legislation. Molsig computes molecular graph descriptors that include stereochemistry information. Currently two property computing tools are provided joelib and open babel. Chemical descriptors are used to calculate and to develop methods for chemical property calculations qspr quantitative structureproperty relationship or chemical activity qsar quantitative structureactivity relationship calculations. These descriptors can be used to evaluate molecular structureactivity or structureproperty relationships, as well as for similarity analysis and highthroughput screening of molecule databases. Oftentimes, descriptors of different nature and origin are mixed together. The open babel tool computes the descriptors currently supported by the open babel software library.
In addition, it provides 59 types of molecular fingerprint systems for drug molecules, including topological fingerprints, electrotopological state estate fingerprints, maccs keys, fp4 keys, atom. You may need a pdf reader to view some of the files on this page. Chemdes is an onlinetool for the calculation of molecular descriptors. Results the software has several advantages over existing standalone molecular descriptor calculation software. Molecular descriptors guide safer chemicals research us epa. The software currently calculates 797 descriptors 663 1d, 2d descriptors, and 4 3d descriptors and 10 types of fingerprints. Descriptors that relate to electronic structure, such as the homo and lumo energies, must be obtained from quantum chemical calculation. Molecular descriptor an overview sciencedirect topics. Which software is best for calculating the molecular descriptor. The webserver is the main entrance for users to calculate molecular descriptors.
The software has several advantages over existing standalone molecular descriptor calculation software. Indexpadeldescchemdeschemdes molecular descriptors computing platform. These descriptors and fingerprints are calculated mainly using the chemistry development kit. However, users of those programs must contend with several issues, including software bugs, insufficient update frequencies, and software licensing constraints. Toxicity estimation software tool test estimates the toxicity values and physical properties of organic chemicals from molecular structure by means of several. Edragon is the electronic remote version of the well known software dragon, which is an application for the calculation of molecular descriptors developed. To address these issues, we propose mordred, a developed. Thevalence chi indices are described on page 86 of the handbook of molecular descriptors todeschiniand consonni 2000. Specifically it calculates almost 4000 descriptors independent of 3dimensional information such as constitutional, topological, phamacophore. Molecular descriptors and fingerprints have been routinely used in qsarsar analysis, virtual drug screening, compound searchranking, drug admet prediction and other drug discovery processes. Computational biology and drug design group,chemdes is an onlinetool for the calculation of molecular descriptors. Czeeks highspeed screening of compoundprotein interactions. Mordred was designed to be a software program that is easy to install and use, supports abundant molecular descriptors, has a high calculation speed, and includes automated tests.
Software for the calculation of structureinformation representation molecular structure descriptors welcome to, home of the molconn indices this authors of this web page are dedicated to advancing the ongoing development and implementation of the structureinformation representation class of molecular structure descriptors. The software currently calculates 8 descriptors 679 1d, 2d descriptors and 4 3d descriptors and 10 types of fingerprints. It is a new cheminformatics tool which transforms a variety of structural features and local environment. Meanwhile, the types of the descriptors are of high diversity.
You can use free online calculation of more than descriptors. Qikprop generates physically relevant descriptors, and uses them to perform admetox predictions. Dragon dragon is an application for the calculation of molecular descriptors. Herein, the user interface of chemdes consists of four main modules. Fast calculation of quantum chemical molecular descriptors from the electronegativity equalization method.
Some descriptors, such as logp and molecular polarizability can be approximated from atomic or group contributions. Code calculation of molecular descriptors please note that corina symphony is the successor of adriana. Software solutions for chemoinformatics and qsar alvascience. Description of the molecular descriptors appearing in the toxicity estimation software tool.
Chemical descriptors are used to calculate and to develop methods for chemical. Molecular descriptor calculations and their application for determining property correlations are described. It currently calculates 797 descriptors 663 1d, 2d descriptors, and 4 3d descriptors and 10 types of fingerprints. There are a number of online websites that provide property calculations, however be careful not to post proprietary information. In addition, it provides 59 types of molecular fingerprint systems for drug molecules, including topological fingerprints, electrotopological state estate fingerprints, maccs keys, fp4 keys, atom pairs. Dragon provides more than 1,600 molecular descriptors that are divided into 20 logical blocks. An approach for developing pharmacophore queries is. Molecular descriptors provide quantitative information about chemical properties of compounds. These descriptors can be used to evaluate molecular structureactivity or structureproperty relationships. The user can calculate not only the simplest atom type, functional. The descriptors and fingerprints are calculated using the chemistry development kit with additional descriptors and fingerprints such as atom type electrotopological state descriptors. Padel is used to calculate molecular descriptors and fingerprints. Specifically it calculates almost 4000 descriptors independent of 3dimensional information such as. The bluedesc descriptor calculator is a commandline tool that converts an mdl sd file into arff and libsvm format using cdk and joelib2 for machine learning and data mining purposes.
Molecular descriptors can be calculated using various software, some of which are listed in table 1 damale et al. To provide an online computing service based on web, the user interface should be convenient and easytouse for the users. Molecular descriptors and fingerprints play an essential role in quantitative structureactivity relationships qsar as they are the mathematical representation of chemicals and they serve as the input for the data analysis methods used to build qsar models. After calculating molecular descriptors these data can be selected as input for various clustering jobs. May 09, 2018 download padeldescriptor software solution that calculates molecular descriptors and fingerprints, its packed with multiple tools and features that you can check out. However, users of those programs must contend with. For comparison purpose, molecular weight, average molecular weight and number of atoms for simple organic molecules calculated by padel, edragon and pydescriptor have. The descriptors and fingerprints are calculated using the chemistry development kit. Cheminformatics 5, 34 20 for calculat molecular descriptors free download sourceforge. Software solution that calculates molecular descriptors and fingerprints, its packed with multiple tools and features that you can check out the internet is filled with all sort of applications. Calculate numerous molecular descriptors of each compound in the datasets. The software currently calculates 797 descriptors 663 1d, 2d descriptors, and 4 3d descriptors and 10 types of.
The calculator plugins, included in the marvin suite, are modules of chemaxons marvin and jchem cheminformatics platforms which calculate chemical. There are many software for the calculation of molecular descriptors that can be used for free. The software can be used on all the major platforms windows, linux, macos and can be deployed using java web start technology. The descriptors and fingerprints are calculated using the chemistry development kit with some additional descriptors and fingerprints.
Integrated computeraided molecular design platform for small molecule and biological therapeutics. His main research activities concern chemometrics in all its aspects, qsar, molecular descriptors, multicriteria decision making and software development. 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. Introductionchemdesmolecular descriptors computing platform. Therefore, there is need for introduction of easily understandable molecular descriptors. Padeldescriptor was developed using the java language and consists of a library and an interface component. It is designed by cbdd group of csu and supply a strong tool of calculating molecular descriptors for researchers. Toxicity estimation software tool test estimates the toxicity values and physical properties of organic chemicals from molecular structure by means of several qsar models.
As pydescriptor is a software plugin dedicated for molecular descriptor calculations only, henceforth its comparisons shall only be made with other similar dedicated software instead of comparing it with general qsar software. Visit the products section for the list of available software. I was surprised to learn that one of the most important molecular descriptors, pka, is not. Tomocomdcardd is an interactive and userfriendly free multiplatform framework designed to calculate 23d numerical descriptors indices for molecular structures, with the objective of characterizing or discriminating among them.
Open source so that researchers could introduce their speci. Contribute to mordred descriptor mordred development by creating an account on github. Common platform for chemists, biologists and crystallographers. Code calculation of molecular descriptors home adriana. Various molecular descriptor calculation software programs have been developed. In the present work, we present a new pymol plugin, pydescriptor, which has capacity to calculate 11,145 easily understandable molecular descriptors.
Dec 17, 2010 it is a multithreaded software which make full use of the multiple cpu cores in modern desktop computers to increase the speed of calculation of molecular descriptors. Introduction padeldescriptor is a software for calculating molecular descriptors and fingerprints. In this chapter we will present alvadesc, a software to calculate and analyze molecular descriptors and fingerprints. You need the molecular structures itself as smiles, sdf in 2d or optimized 3d structure. Here you can find a list of some projects that can be directly used on the web and exploit dragon for the calculation of molecular descriptors.
Molecular descriptors are widely employed to present molecular characteristics in cheminformatics. Descriptor is a software for calculating molecular descriptors and fingerprints. Cuct a reliable model of the training dataset to predict the target activyoperyrom these calculated descriptors using classi. Chemical computing group ccg computeraided molecular. 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. Abstract due to the relevance that molecular descriptors are constantly gaining in several scientific fields, software for the calculation of molecular descriptors have become very important tools. The software currently calculates 863 descriptors 729 1d, 2d descriptors and 4 3d. Can molecular descriptors be calculated with schrodinger. This site provides free online tools, which are helpful in performing computational chemistry, admet and chemoinformatics tasks including the building and visualisation of chemical structures, the calculation of molecular properties and the analysis of relationships between chemical structure and properties.
Dragon is the worldwide most used application for the calculation of molecular descriptors. A software to calculate molecular descriptors and fingerprints. Padel descriptor was developed using the java language and consists of a library and an interface component. It computes 174 descriptors taken from both libraries. The joelib tool computes 38 descriptors for each compound, which are described in detail here. Dragon calculation of molecular descriptors and fingerprints.
Roberto todeschini is full professor of chemometrics at the department of environmental sciences of the university of milanobicocca, where he constituted the milano chemometrics and qsar research group. Projects with dragon dragon is used as a part of several qsar modelling applications and suites, as well as in scientific studies. Handling the molecules together with all descriptors can be a challenging task, software which can do that is highly preferred. Journal of chemical information and computer sciences 2003, 43 2, 422428. The molecular descriptor correlations is a free tool for the analysis of molecular descriptor correlations calculated on 221,860 molecules from the nci database. Pfas carbonfluorine bond descriptors this is a modified java code based on the approach in j. Molecular descriptor calculation programs usually have many dependent software programs that must be. The www as a tool to obtain molecular parameters, mini rev med chem, 2003, 38, 80920, article. They can be very useful for prioritizing lead compounds, property clustering and qsar analyses. It is reasonable that a good descriptor calculation software should have following features 19. Descriptors calculated using multiple conformations, orientations, protonation states and isosteriomers of the ligand constitute 5d descriptors. According todeschini and consonni chemical descriptor is the molecular descriptor is the final result of a logic and mathematical procedure which transforms chemical information encoded within a symbolic representation of a molecule into a useful number or the result of some standardized experiment. Qsar suites molecular descriptors calculation dragon talete srl. Online software virtual computational chemistry laboratory.
Dec 17, 2010 the software uses a masterworker pattern to take advantage of the multiple cpu cores that are present in most modern computers to speed up calculations of molecular descriptors. Thesimple chi indices are described on page 85 of the handbook of molecular descriptors todeschiniand consonni 2000. This site also performs online calculation of molecular descriptors using edragon using clientserver interface to the dragon software of prof. The software uses a masterworker pattern to take advantage of the multiple cpu cores that are present in most modern computers to speed up calculations of molecular descriptors.
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