Review Article

An Updated Review of Computer-Aided Drug Design and Its Application to COVID-19

Table 4

List of programs available for calculating molecular descriptors for building QSAR models.

ProgramsMolecular descriptorsReference

ADMET PredictorPredicts over 140 properties such as solubility, logP, pKa, sites of CYP metabolism, and Ames mutagenicity.https://www.simulations-plus.com/software/admetpredictor/

ChemAxonIt provides a wide range of chemical calculations such as molecular weight, elemental composition, LogP, pKa, LogD, LogS, hydrogen bond donor/acceptor (HBDA) count, and various 2D topological descriptors and 3D geometrical descriptors.https://chemaxon.com/products/calculators-and-predictors

PaDEL-DescriptorPaDEL-descriptor is a standalone software for calculating molecular descriptors and fingerprints including 797 descriptors (663 1D, 2D descriptors, and 134 3D descriptors) and 10 types of fingerprints.[101]

E-DRAGONE-DRAGON is the electronic remote version of the noted software DRAGON, which is an application for the calculation of molecular descriptors (>1,600 molecular descriptors) used for evaluating molecular structure-activity or structure-property relationships.http://www.vcclab.org/lab/edragon/

DRAGON 7.0Dragon 7.0 calculates 5,270 molecular descriptors including the simplest atom types, functional groups and fragment counts, topological and geometrical descriptors, and three-dimensional descriptors which are organized into thirty logical blocks.https://chm.kode-solutions.net/products_dragon.php

CODESSA PROCODESSA PRO (comprehensive descriptors for structural and statistical analysis) is an extensive program for studying quantitative structure-activity/property relationships (QSAR/QSPR) by facilitating the calculation of a wide range of molecular descriptors derived from the 2D/3D geometrical structure and/or quantum-chemical wave function of small molecules.[102]

Pre-ADMETPreADMET is a web-based program that can be used for the calculation of drug-like physicochemical descriptors such as lipophilicity (logP), molecular weight, polar surface area, and water solubility.https://preadmet.bmdrc.kr/

QikPropQikProp program allows the prediction of various pharmacologically important descriptors of chemical compounds such as octanol/water and water/gas log Ps, log S, log BB, overall CNS activity, Caco-2, and MDCK cell permeabilities, log KHSA for human serum albumin binding, etc.https://www.schrodinger.com/qikprop

ACD/labsACD/labs is a multipurpose tool that can be used for the calculation of a variety of physicochemical descriptors such as aqueous solubility, boiling point/vapour pressure, logD, logP, and pKa and ADME properties.https://www.acdlabs.com/

Corina SymphonyCORINA symphony is a cheminformatic tool for structure representation and calculation of molecular descriptors of six types: global molecular descriptors, shape descriptors, quantum-mechanical properties, 2D property-weighted autocorrelation, 3D property-weighted autocorrelation, property-weighted radial distribution functions (RDF), and autocorrelation of surface properties.https://www.mn-am.com/products/corinasymphony

MOPACMOPAC (molecular orbital PACkage) is a semiempirical molecular orbital package for studying solid-state and molecular structures and reactions and offers calculations of various descriptors of molecules, radicals, ions, and polymers such as the vibrational spectra, thermodynamic parameters, isotopic substitution effects, and force constants.http://openmopac.net/