Jun 05, 2019 moriwaki h, tian ys, kawashita n, takagi t 2018 mordred. In addition, it provides 59 types of molecular fingerprint systems for drug molecules, including topological fingerprints, electrotopological state e. Calculate numerous molecular descriptors of each compound in the datasets. A molecular descriptor is a structural or physicochemical property of a molecule or part of a molecule.
Molecular visualization freeware for proteins, dna and macromolecules. Descriptors calculated from 3d structures may require the analysis of many molecular conformations, provided that biologically active conformations are not known from. May 09, 2018 download padel descriptor software solution that calculates molecular descriptors and fingerprints, its packed with multiple tools and features that you can check out. Padel software tutorial calculating descriptors youtube. It provides almost 5,000 molecular descriptors of different types. Definition of molecular descriptordefinition of molecular descriptor 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. Prodrg, a program for generating molecular topologies and. A selection of commercial and free descriptor calculation utilities is collected under the molecular descriptor software collection or the. Quantitative structureactivity relationship models qsar models are regression or classification models used in the chemical and biological sciences and engineering. Molecular descriptors are either twodimensional 2d or threedimensional 3d todeschini et al.
An important feature of grind is that, with the use of appropriate software, the original descriptors molecular interaction fields can be regenerated from the autocorrelation transform and, thus, the results of the analysis represented graphically, together with the original molecular structures, in 3d. See the e3fp paper repository for an application 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. Download padel descriptor software solution that calculates molecular descriptors and fingerprints, its packed with multiple tools and features that you can check out. The descriptor aims to measure the deviation from an overall symmetric shape of the molecule.
Like other regression models, qsar regression models relate a set of predictor variables x to the potency of the response variable y, while classification qsar models relate the predictor variables to a categorical value. There are currently a large number of molecular descriptors, which can be classified into three broad categories. To address these issues, we propose mordred, a developed. In this sense, descriptors can show no degeneracy at all, low, intermediate, or high degeneracy. Various molecular descriptor calculation software programs have been developed. Distributed by compudrug brief description codessa pro tm comprehensive descriptors for structural and statistical analysis is a comprehensive program for developing quantitative structureactivityproperty relationships qsarqspr that integrates all necessary mathematical and computational tools to calculate a large variety of molecular descriptors on the basis of the 2d 3d. The molecules are mainly collected from the nci database, while the molecular descriptors have been calculated by means of dragon. These descriptors and fingerprints are calculated mainly using the chemistry development kit. E3fp is a 3d molecular fingerprinting method inspired by extended connectivity fingerprints ecfp, integrating tightly with the rdkit documentation is hosted by readthedocs, and development occurs on github installation and usage.
Molecular descriptors and fingerprints have been routinely used in qsarsar analysis, virtual drug screening, compound searchranking, drug admet prediction and other drug discovery processes. However, all quantum chemical and most molecular descriptor calculation programs require the 3d representation of molecular structures as an input. Thesimple chi indices are described on page 85 of the handbook of molecular descriptors todeschiniand consonni 2000. The molecular descriptor correlations is a free tool for the analysis of molecular descriptor correlations calculated on 221,860 molecules from the nci database. The screening of chemical libraries with traditional methods, such as highthroughput screening hts, is expensive and time consuming. It is reasonable that a good descriptor calculation software should have following features 19. Integrated computeraided molecular design platform. Here we propose a novel 3d qsar descriptor termed enantioselective molecular asymmetry emas that is capable of distinguishing between enantiomers in the absence of such heuristics. Open source molecular modeling about open source molecular modeling here we maintain an updateable catalog of open source molecular modeling software, initially taken from our paper. Chemical descriptors are used to calculate and to develop methods for chemical. Introductionchemdesmolecular descriptors computing platform. Cuct a reliable model of the training dataset to predict the target activyoperyrom these calculated descriptors using classi. These descriptors and fingerprints are calculated mainly using the.
Some commonly used methods for calculating 3d descriptors are comfa, comsia, combine, germ, comma, grind, whim, holoqsar and cosa. The software currently calculates 863 descriptors 729 1d, 2d descriptors and 4 3d. Molecular descriptors are experimentallymeasured or theoreticallyderived properties of a molecule. One of four chains in oxyhemoglobin zooming in to oxyheme from 1hho. Introduction padel descriptor is a software for calculating molecular descriptors and fingerprints. The program starts from a set of structures, computing highly relevant 3d maps of interaction energies between the molecule and chemical probes grid based molecular interaction fields, or mifs. In descriptor based machine learning approaches, a large number of descriptors are fed into the model as input comprising zero, one, two, and threedimensional 0d, 1d, 2d, and 3d molecular. Dragon is the most used software for molecular descriptors. Morse, which encode multiple physicochemical and structural properties of a compound.
Molecular descriptors derived from atomic or molecular properties that translate physicochemical, topological, and surface properties of. A software to calculate molecular descriptors and fingerprints. The invariance properties of molecular descriptors can be defined as the ability of the algorithm for their calculation to give a descriptor value that is independent of the particular characteristics of the molecular representation, such as atom numbering or labeling, spatial reference frame, molecular conformations, etc. A selection of commercial and free descriptor calculation utilities is collected under the molecular descriptor software collection or the compchem list or new programs are posted to ccl. It calculates 797 descriptors 663 1d, 2d descriptors and 4 3d descriptors and 10 types of fingerprints. This framework is comprised of two suites with parallel functionalities. It is better to do this job using your own means than to rely on this software to do it. To run dragon the user needs molecular structure files previously obtained by other specific molecular modelling software.
For more information about this descriptor, see hill 1960. Mar 20, 2018 the check and preprocessing for various molecular objects is of high importance for subsequent descriptor calculation and data analysis, especially those molecular objects from web sources. Qsar classification models for predicting the activity of. In edragon, if the 3d atom coordinates are not available for molecules, the. Quantitative structureactivity relationship wikipedia. Dragon requires 3d optimised structures with hydrogens. I was surprised to learn that one of the most important molecular descriptors, pka, is not provided by dragon 7 or alvadesc 1. Journal of computational chemistry 2011, 32 7, 14661474. Pentacle is an advanced software tool for obtaining alignmentindependent 3d quantitative structureactivity relationships. The threedimensional coordinates of small molecules can be converted to molecular descriptor strings that encode them uniquely in order to enable smallmolecule recognition, despite. Molecular topology files for many molecular modeling programs can be generated automatically. A qsar model for predictive toxicology is a mathematical relationship between a chemicals quantitative molecular descriptors and its toxicological endpoint 9,44. It computes 1875 descriptors 1444 1d, 2d descriptors and 431 3d descriptors and 12 types of fingerprints.
The whole process of calculating 3d molecular descriptors is nearly the same with that of calculating 1d2d molecular descriptors. The main basis that we divide these molecular descriptors into 20 logical blocks is as follows. The software currently calculates 8 descriptors 679 1d, 2d descriptors and 4 3d descriptors and 10 types of fingerprints. Openmolgrid open computing grid for molecular science. One suite is made up of a set of modules derived from algebraic considerations.
These molecular descriptors can be used to evaluate molecular structureactivityproperty relationships of. The molecular volume is calculated as a function of conformation. More specifically, they are quantitative representations of physical, chemical or topological characteristics of molecules that summarize our knowledge and understanding of molecular structure and activity from different aspects. Padel descriptor calculates molecular descriptors and fingerprints. It analyzed all the molecules from nci dataset in order to. Rdkit is a quick and free way to get a bunch of descriptors, which range from 1d to 3d. Free descriptors generator software for fastcalculating descriptors from a twodimensional chemical structure that is suitable for small and large datasets. Quantitative structureproperty relations qspr employing descriptors derived from the 3d molecular structure are frequently applied for property prediction in various fields of research.
Molecular volume vm a 3d spatial descriptor that defines the molecular volume inside the contact surface. Edragon software virtual computational chemistry laboratory. Also, note that if your molecular names are not completely niche, you can easily convert them into smiles. Molecular descriptor correlations is a free tool for the analysis of molecular descriptor correlations calculated on 221,860 molecules. Dragon, moe, modesla, mopac software packages, and statistica software version 8. Converter form 2d smiles structures to 3d structures. Molecular descriptors calculation dragon talete srl. Tomocomdcardd is an interactive and userfriendly free multiplatform framework designed to calculate 2 3d numerical descriptors indices for molecular structures, with the objective of characterizing or discriminating among them.
It calculates a comprehensive collection of more than 5000 molecular descriptors 0d, 1d, 2d, 3d 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 by the milano chemometrics and qsar research group of prof. These last invariance properties are required for the 3ddescriptors. Aug 19, 2017 this video is the the tutorial on how to calculate the descriptors using padel software. Descriptor is a software for calculating molecular descriptors.
Dragon is the worldwide most used application for the calculation of molecular descriptors. Journal of chemical information and computer sciences 2004, 44 2, 658668. Open source so that researchers could introduce their speci. Moriwaki h, tian ys, kawashita n, takagi t 2018 mordred. Check the list of descriptors, 3d descriptors and fingerprints here. Molecular descriptor an overview sciencedirect topics. In this report, we introduce a set of aggregation operators aos to calculate global and local group and atom type molecular descriptors mds as a generalization of the classical approach of molecular encoding using the sum of the atomic or fragment contributions. You just need a training set of molecules with activity data. Some molecules may contain structure defects to a certain extent, and therefore seriously influence or even destroy the subsequent descriptor calculation.
The program starts from a set of structures, computing highly relevant 3d maps of interaction energies between the molecule and chemical probes grid based molecular. In edragon the accepted molecular structure files smiles, sdf mdl or mol2 sybyl files. For example, some implicit 3d descriptors representing surface area terms or shape indices can be calculated from 2d representations of molecules or molecular graphs 2. We introduce the 3d zernike descriptor 3dzd, an emerging technique to describe molecular surfaces. When global and local molecular descriptors are more than. The software currently calculates 797 descriptors 663 1d, 2d descriptors, and 4 3d descriptors and 10 types of fingerprints.
Mole db molecular descriptors data base is a free online database comprised of 1124 molecular descriptors calculated for 234773 molecules. Molecular volume is related to binding and transport. The density reflects the types of atoms and how tightly they are packed in a molecule. On the other hand, molecular docking studies provide the possible. Molecular modeling approaches for the discovery of. This property refers to the ability of a descriptor to avoid equal values for different molecules. The descriptors and fingerprints are calculated using the chemistry development kit with some additional descriptors and fingerprints. Molecular descriptors available on this page keywords basis.
Molecular descriptors are formally mathematical representations of a molecule obtained by a wellspecified algorithm applied to a defined molecular representation or a wellspecified experimental procedure. The 3dzd is a series expansion of mathematical threedimensional function, and thus a tertiary structure is represented compactly by a vector of coefficients of terms in the series. For the generation of the independent variables descriptors, the most stable structures obtained in section 2. Qubilsmidas a highly parallel software for threedimensional molecular descriptor calculations concepts for descriptor calculations and qsarqspr modeling. However, users of those programs must contend with several issues, including software bugs, insufficient update frequencies, and software licensing constraints. Kode chm chemoinformatics consultancy and software development for industry and research.
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. Specifically it calculates almost 4000 descriptors independent of 3dimensional information such as constitutional, topological, phamacophore. Toxmatch toxmatch is a flexible and userfriendly opensource software application that encodes several chemi. A software package is described that operates on small molecules observed in the pdb collection of protein structures. You can obtain the 3d molecule via chemmop if you wish to compute 3d descriptors using molecule without 3d structure and check the option of no, chemdes will force to use mm2 forcefield. Structureresponse correlations and similaritydiversity. Molsig computes molecular graph descriptors that include stereochemistry information. Molecular descriptors are widely employed to present molecular characteristics in cheminformatics. Threedimensional quantitative structure activity relationships, vol 2. You need a large dataset with the molecular property logp, bp to be modeled. The software currently calculates 1875 descriptors 1444 1d, 2d descriptors and 431 3d descriptors and 12 types of fingerprints total 16092 bits.
After selecting descriptors, a kind of forcefield for mopac optimization is needed and must be chosen from the dropdown menu. In particular, dragonx is one of the most widely used software packages for descriptor calculation. Descriptors and their selection methods in qsar analysis. Effect of coordinate rotation on 3d molecular descriptors. For installation and usage instructions, see the documentation. Molecular descriptor correlations free download and. Free or lowpriced so that it is easy to purchase it. Which software is best for calculating the molecular descriptor.
An open source software to calculate molecular descriptors and fingerprints. The molecular descriptor is the final result of a logic and mathematical procedure which transforms chemical information encoded within a symbolic representation of. Software solutions for chemoinformatics and qsar alvascience. A 3d spatial descriptor that is defined as the ratio of molecular weight to molecular volume. Various moleculardescriptorcalculation software programs have been. Padel is used to calculate molecular descriptors and fingerprints. The mole db molecular descriptors data base is a free online database constituted of.
Bclemas enantioselective molecular asymmetry descriptor. The mopac version 7 software has been adapted for the semiempirical quantum chemical calculations. Dragon provides more than 1,600 molecular descriptors that are divided into. Description a software to calculate molecular descriptors and fingerprints. New molecular descriptors based on local properties at the molecular surface and a boilingpoint model derived from them. Accessing the antiproliferating activity of tankyrase2. The most common molecular file formats are accepted. Computeraided molecular modeling studies of some 2, 3. Descriptor is a software for calculating molecular descriptors and fingerprints. Specifically it calculates almost 4000 descriptors independent of 3dimensional information such as. Joining tree clustering jtc, kmeans cluster analysis and molecular descriptor calculations.
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