Visit the products section for the list of available software. Some descriptors, such as logp and molecular polarizability can be approximated from atomic or group contributions. Molecular descriptors provide quantitative information about chemical properties of compounds. You need the molecular structures itself as smiles, sdf in 2d or optimized 3d structure. His main research activities concern chemometrics in all its aspects, qsar, molecular descriptors, multicriteria decision making and software development. 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 is the worldwide most used application for the calculation of molecular descriptors. I was surprised to learn that one of the most important molecular descriptors, pka, is not. Czeeks highspeed screening of compoundprotein interactions.
Contribute to mordred descriptor mordred development by creating an account on github. 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. Thesimple chi indices are described on page 85 of the handbook of molecular descriptors todeschiniand consonni 2000. It currently calculates 797 descriptors 663 1d, 2d descriptors, and 4 3d descriptors and 10 types of fingerprints. 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. 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. It calculates a comprehensive collection of more than 5000 molecular descriptors 0d, 1d, 2d, 3d molecular descriptors. 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. Molecular descriptor calculations and their application for determining property correlations are described. Molecular descriptor calculation programs usually have many dependent software programs that must be. Molecular descriptors and fingerprints have been routinely used in qsarsar analysis, virtual drug screening, compound searchranking, drug admet prediction and other drug discovery processes. It computes 174 descriptors taken from both libraries. Recently, webbased descriptor generation tools have been proposed as well.
Code calculation of molecular descriptors home adriana. The software has several advantages over existing standalone molecular descriptor calculation software. I have to calculate the molecular descriptor using freeware. Software solutions for chemoinformatics and qsar alvascience. Introduction padeldescriptor is a software for calculating molecular descriptors and fingerprints. Descriptors that relate to electronic structure, such as the homo and lumo energies, must be obtained from quantum chemical calculation.
The descriptors and fingerprints are calculated using the chemistry development kit with additional descriptors and fingerprints such as atom type electrotopological state descriptors. You may need a pdf reader to view some of the files on this page. Thevalence chi indices are described on page 86 of the handbook of molecular descriptors todeschiniand consonni 2000. Dragon dragon is an application for the calculation of molecular descriptors. Introductionchemdesmolecular descriptors computing platform. Fast calculation of quantum chemical molecular descriptors from the electronegativity equalization method. 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. The software can be used on all the major platforms windows, linux, macos and can be deployed using java web start technology. Code calculation of molecular descriptors please note that corina symphony is the successor of adriana. Molecular descriptors are widely employed to present molecular characteristics in cheminformatics. The webserver is the main entrance for users to calculate molecular descriptors. 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. Online software virtual computational chemistry laboratory.
Descriptor is a software for calculating molecular descriptors and fingerprints. 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. The descriptors and fingerprints are calculated using the chemistry development kit. For comparison purpose, molecular weight, average molecular weight and number of atoms for simple organic molecules calculated by padel, edragon and pydescriptor have. The software currently calculates 797 descriptors 663 1d, 2d descriptors, and 4 3d descriptors and 10 types of. Molsig computes molecular graph descriptors that include stereochemistry information. Qsar suites molecular descriptors calculation dragon talete srl. In this chapter we will present alvadesc, a software to calculate and analyze molecular descriptors and fingerprints. The open babel tool computes the descriptors currently supported by the open babel software library. Open source so that researchers could introduce their speci.
Specifically it calculates almost 4000 descriptors independent of 3dimensional information such as. Edragon software virtual computational chemistry laboratory. Molecular descriptor an overview sciencedirect topics. These descriptors and fingerprints are calculated mainly using the chemistry development kit. 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.
It is a new cheminformatics tool which transforms a variety of structural features and local environment. You can use free online calculation of more than descriptors. Currently two property computing tools are provided joelib and open babel. Chemdes is an onlinetool for the calculation of molecular descriptors. These descriptors can be used to evaluate molecular structureactivity or structureproperty relationships. Toxicity estimation software tool test estimates the toxicity values and physical properties of organic chemicals from molecular structure by means of several. The user can calculate not only the simplest atom type, functional. Common platform for chemists, biologists and crystallographers.
Chemical computing group ccg computeraided molecular. Free or lowpriced so that it is easy to purchase it. 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. Therefore, there is need for introduction of easily understandable molecular descriptors. Oftentimes, descriptors of different nature and origin are mixed together. Molecular descriptors guide safer chemicals research us epa.
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. Description of the molecular descriptors appearing in the toxicity estimation software tool. The joelib tool computes 38 descriptors for each compound, which are described in detail here. Can molecular descriptors be calculated with schrodinger. To address these issues, we propose mordred, a developed.
An approach for developing pharmacophore queries is. Meanwhile, the types of the descriptors are of high diversity. 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. Toxicity estimation software tool test estimates the toxicity values and physical properties of organic chemicals from molecular structure by means of several qsar models.
Molecular descriptors can be calculated using various software, some of which are listed in table 1 damale et al. The software currently calculates 1875 descriptors 1444 1d, 2d descriptors and 431 3d descriptors and 12 types of fingerprints total 16092 bits. 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. This site also performs online calculation of molecular descriptors using edragon using clientserver interface to the dragon software of prof. There are a number of online websites that provide property calculations, however be careful not to post proprietary information. The software currently calculates 863 descriptors 729 1d, 2d descriptors and 4 3d. Padeldescriptor was developed using the java language and consists of a library and an interface component.
Various molecular descriptor calculation software programs have been developed. 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. They can be very useful for prioritizing lead compounds, property clustering and qsar analyses. Handling the molecules together with all descriptors can be a challenging task, software which can do that is highly preferred. Integrated computeraided molecular design platform for small molecule and biological therapeutics. 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. Dragon provides more than 1,600 molecular descriptors that are divided into 20 logical blocks. 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. Edragon is the electronic remote version of the well known software dragon, which is an application for the calculation of molecular descriptors developed. There are many software for the calculation of molecular descriptors that can be used for free.
Journal of chemical information and computer sciences 2003, 43 2, 422428. However, users of those programs must contend with several issues, including software bugs, insufficient update frequencies, and software licensing constraints. Descriptors calculated using multiple conformations, orientations, protonation states and isosteriomers of the ligand constitute 5d descriptors. The www as a tool to obtain molecular parameters, mini rev med chem, 2003, 38, 80920, article. Herein, the user interface of chemdes consists of four main modules. Projects with dragon dragon is used as a part of several qsar modelling applications and suites, as well as in scientific studies. However, users of those programs must contend with. The cheminformatics program canvas has a molecular descriptors application, and there is a script on the scripts menu in maestro.
Cheminformatics 5, 34 20 for calculat molecular descriptors free download sourceforge. 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. Padel is used to calculate molecular descriptors and fingerprints. Padel descriptor was developed using the java language and consists of a library and an interface component. The calculator plugins, included in the marvin suite, are modules of chemaxons marvin and jchem cheminformatics platforms which calculate chemical.
Which software is best for calculating the molecular descriptor. Molecular alignments and conformational analyses of a congeneric series are explored to assess the impact of ligand substituents. It is reasonable that a good descriptor calculation software should have following features 19. Cuct a reliable model of the training dataset to predict the target activyoperyrom these calculated descriptors using classi.
Calculate numerous molecular descriptors of each compound in the datasets. The molecular descriptor correlations is a free tool for the analysis of molecular descriptor correlations calculated on 221,860 molecules from the nci database. 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. 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. Results the software has several advantages over existing standalone molecular descriptor calculation software. Specifically it calculates almost 4000 descriptors independent of 3dimensional information such as constitutional, topological, phamacophore.
Cbddgroupcomputational biology and drug design group. These descriptors can be used to evaluate molecular structureactivity or structureproperty relationships, as well as for similarity analysis and highthroughput screening of molecule databases. Qikprop generates physically relevant descriptors, and uses them to perform admetox predictions. After calculating molecular descriptors these data can be selected as input for various clustering jobs. 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. It is designed by cbdd group of csu and supply a strong tool of calculating molecular descriptors for researchers. 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. Indexpadeldescchemdeschemdes molecular descriptors computing platform. 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.
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. This practically oriented reference book gives a thorough overview of the different molecular descriptors representations and their corresponding molecular descriptors. The software currently calculates 8 descriptors 679 1d, 2d descriptors and 4 3d descriptors and 10 types of fingerprints. To provide an online computing service based on web, the user interface should be convenient and easytouse for the users. Various moleculardescriptorcalculation software programs have been developed. Padeldescriptor is a software for calculating molecular descriptors and. The software currently calculates 797 descriptors 663 1d, 2d descriptors, and 4 3d descriptors and 10 types of fingerprints. You need a descriptor package for descriptor calculation. In the present work, we present a new pymol plugin, pydescriptor, which has capacity to calculate 11,145 easily understandable molecular descriptors. Computational biology and drug design group,chemdes is an onlinetool for the calculation of molecular descriptors.