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An Introduction to the Basic Concepts in QSAR-Aided Drug Design
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KEY TERMS AND DEFINITIONS
3D-QSAR: Quantitative analysis of relationship between spatial features of a set of compounds and
biological activities using statistical methods.
Accuracy: The accuracy of a predicted model, the most important quality measurement, is usually
calculated for both training and test sets.
Dimensionality Reduction: A transformation function/algorithm which maps a large dataset of
descriptors in to a small dataset of descriptors as a representative subset of the large dataset. The algorithms can be either linear or non-linear.
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An Introduction to the Basic Concepts in QSAR-Aided Drug Design
Machine Learning: An important field of artificial intelligence in computer science is the machine
learning. Machine learning algorithms are diverse and are used to extract the rules of black box functionality
by mapping the inputs to the corresponding outputs using the computational and statistical calculations.
Molecular Descriptor: Numerical representation of molecular properties (e.g. physicochemical
properties) of chemical structures.
Pharmacophore: Minimum structural requirement of a compound necessary for interaction with a
target molecule.
QSAR: Quantitative correlation between biological activities of compounds and chemical structures
represented by a regression model.
Test Data Set: A set of compounds which does not have any role in training process and is used for
model evaluation.
Training Data Set: A set of molecules selected for training of the model using machine learning
algorithms.
ENDNOTES
1
Tripos is a well-known and global pioneer in computational drug discovery capabilities by design-
ing and development of scientific software products. http://www.tripos.com
2
Advanced Chemistry Development, Inc., (ACD/Labs) is one of the companies providing chemistry
software for data management and informatics. ACD/Labs suite of programs provide in silico pre-
diction of molecular physical properties and ADMET property. ACD/Labs Release 2014 (v2014)
software is the latest version.http://www.acdlabs.com/
3
CambridgeSoft was a cheminformatics software company. In 2011, the company was sold to
PerkinElmer, a laboratory instruments company. The collection of programs supplies the chemical
structures and their associated data and properties.http://www.cambridgesoft.com/
4
InfoChem is a collection of software tools and applications for chemical data management, stor-
age, handling and retrieval of structures and reactions.http://www.infochem.de/
5
Dragon was developed by an Italian company, namely, Talete. It is designed for calculation of
molecular descriptors which can be used in QSAR studies. The latest version is Dragon 6. It can
be found at:http://www.talete.mi.it/products/dragon_description.htm
6
PubChem was released in 2004 as a database within national center for biotechnology information
(NCBI) for providing information on chemical structure and biological activities of small molecules.
7
ChemDraw is a chemical drawing tool for generating images of manuscripts, databases, and mak-
ing useful queries in chemical databases
https://www.cambridgesoft.com/Ensemble_for_Chemistry/ChemDraw/
8
ACD/ChemSketch is a drawing package that includes drawing and calculation of chemical struc-
tures and molecular properties, and prediction of logP.
http://www.acdlabs.com/resources/freeware/chemsketch/
9
Open Babel is a free chemical toolbox designed to search, convert, analyze, or store data from
molecular modeling and related areas. http://openbabel.org/wiki/Main_Page
10
CORINA is useful in generating 3D structure for small and medium sized molecules.
https://www.molecular-networks.com/products/corina
11
Concord which is included in SYBLE is used for equality assessments on every structures in 3D.
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