BIOINFORMATICS & CHEMOINFORMATICS

Purna Nagasree Kurre*, Raaga Sree Bade, Srinu Talla , Krishna

Department of Pharmaceutical Chemistry & Analysis, Raghu College of Pharmacy , Dakamari, India
*Corresponding Author: Mrs. Purna Nagasree Kurre: E Mail: [email protected]
ABSTRACT:

The multidisciplinary areas of bioinformatics and chemoinformatics use computer methods to

analyse and understand data related to biology and chemistry, respectively. The field of
bioinformatics is concerned with processing and comprehending complex biological datasets,
such as those including genomic, proteomic, and transcriptomic data, by using software tools,
statistical models, and algorithms. It is essential to fields like molecular modelling,
personalised medicine, and gene discovery to make for more efficient and easier. Contrarily,
cheminformatics uses computational techniques to address chemical issues, mainly in drug
development, molecular design, and chemical compound analysis. Both fields contribute to
advances in pharmaceutical development, biomedical research, and the understanding of
molecular interactions by integrating data from various sources and utilising machine
learning and data mining techniques. This ultimately drives innovation in healthcare and
therapeutic interventions. This review article gives an overview about the various data bases
available and briefly describes about their key roles, features and compatibility.

Keywords: Bioinformatics, Chemoinformatics, Software, Computational techniques, Drug

development, & Biomedical research.

INTRODUCTION:

Bioinformatics is an interdisciplinary discipline that lies at the interface of computer science

and biological sciences. Despite the lack of a clear definition for the term, one might argue
that the scientific field of "bioinformatics" is concerned with the computerised management
of many kinds of molecular biological information. Biological information organisation and
biological data analysis make up the bulk of research activity in bioinformatics. Most modern
bioinformatics endeavours concentrate on the structural and functional characteristics of
genes and proteins since molecular biology generates a vast amount of data [1,2].

The use of computer and informational tools to various chemistry-related issues is known as
cheminformatics. These methods, which are also referred to as chemical informatics and
cheminformatics, are employed by pharmaceutical companies in the drug discovery process.
Cheminformatics is the interdisciplinary study of chemical science and computer science,
with a focus on chemical graph theory and chemical space mining. It is predicted that there
are at least 1062 molecules in the chemical universe [2,3].

General Concept of Bioinformatics:

The following can be used to further explain the broad idea of bioinformatics: A combination
of Computer Science, Molecular Biology, and Biochemistry. Acquiring, preserving,
classifying, and evaluating genetic and biological data in order to comprehend how it
functions in living things. Transforming a vast amount of complicated data into knowledge
and information that is helpful is the primary objective of bioinformatics. Nucleotide
sequences, cDNA, and gene and protein sequences are examples of data. Information
gathered through various research approaches such as combinatorial chemical synthesis,
proteomics, pharmcogenomics, gene-expression studies, and gene sequencing. Data that is
utilised to create artificial and forecast models that help scientists comprehend intricate
biological processes [3,4].

Fig. 1. Basic Components of Bioinformatics [3]

General Concept of Chemoinformatics:

The word "cheminformatics" refers to a broad category that includes the development,
production, arrangement, administration, retrieval, analysis, distribution, visualisation, and
use of chemical information. Typical examples of chemical data of interest are small
molecule formulae, structures, properties, spectra, and activities (industrial or biological). It
started out as a tool to help with drug discovery and development, but now days, its
importance has increased many times over, becoming a crucial part of many areas of
chemistry, biochemistry, and biology. The first and most crucial step in the discovery of
small-molecule drugs is the identification of hits. Using virtual chemical libraries in various
virtual screening techniques has emerged as a viable strategy for finding new hit compounds
[4,5,6]
.

Fig. 2. Drug Discovery Steps Using Bio- & Chemoinformatic Tools [7]

Aims of Bioinformatics:

Three primary goals comprise bioinformatics.

1. Firstly, to put things simply, bioinformatics is the organisation of data so that

researchers may access current information and contribute new items as they are
discovered (for instance, for 3D macromolecular structures there is the Protein Data
Bank).
2. While data preservation is important, the information stored in these databases is
essentially useless unless it is examined. Thus, developing tools and technology that
enable data analysis is the objective of the second purpose.
3. The final objective is to use these instruments to assess the information and interpret
the results in a way that makes biological sense.
Historically, biological science has examined certain systems in great detail and has
drawn similarities with a small number of related ones. In bioinformatics, global
evaluations of all the data are carried out with the aim of emphasising features unique to
certain systems and finding patterns common to many systems [8,9].
MATERIALS AND METHODS:

a) Bioinformatics Tools:
A new field of study has been made possible by the use of bioinformatics tools in the
drug creation process. Computational approaches, on the other hand, help in drug target
searches and in silico drug design, although they are time and cost-consuming.
The following steps must be taken in order to create a novel medication,
1.Determine the disease of interest
2. Research intriguing substances
3. Finding the molecular causes of illness
4. Reasonable methods for creating pharmaceuticals
5. Compound refinement
6. QSAR (Quantitative Structure Activity Relationship)
7. The molecule's solubility
8. Testing for drugs

1. Determine the disease of interest:

Target identification on its own is insufficient for an illness to be successfully treated.
A legitimate medication must be created. One must be well informed about the illness
and any current or conventional treatments. It's also critical to examine closely related
illnesses and available therapies. The target protein must be influenced by this
medication in a way that avoids interfering with regular metabolism. The
development of bioinformatics methods allows for a virtual screening of the target for
substances that bind to and inhibit proteins.

2. Research intriguing substances:

Finding and researching the lead chemicals with some anti-disease action is
necessary. These could have serious negative effects and be just mediocrely helpful.
These substances offer a foundation for further chemical structure refinement.
3. Finding the molecular causes of illness:
A medication can be specifically designed to bind at a specific place if it is known
that the medicine must attach to a certain protein or nucleotide. This is frequently
done computationally using a variety of methods. In the past, the research team's
comprehension of chemical interactions served as the main basis for choosing which
 compounds to test computationally. Using a database of accessible structures, a large
number of compounds may be brute-force tested as a second approach.

4. Reasonable methods for creating pharmaceuticals:

These methods make an effort to replicate the understanding of the researchers about
the selection of likely compounds, and they are integrated into a software package that
can automatically model a vast number of compounds. For this kind of testing, a wide
variety of algorithms have been employed, many of which were modified from
artificial intelligence applications. The structures of bigger macromolecules are
difficult to establish due to the complexity of biological systems.

5. Compound refinement:
Computational and laboratory approaches have proven to be highly effective in
improving the molecular structures of lead compounds, resulting in increased
therapeutic action and reduced adverse effects. carried both computationally and in
the lab by looking at the molecular structures to identify the components that are in
charge of the drug's action as well as its adverse effects.

6. QSAR (Quantitative Structure Activity Relationship):

To improve your medication, you should employ computational methods to identify
the functional group in your chemical.

7. The Molecule's Solubility:

It is important to determine if the target molecule is easily soluble in fat or water
because this will determine which area of the body it concentrates in.

8. Testing for Drugs:

A medicine must undergo extensive testing before it can be administered to human
patients, even after an early assay approach has demonstrated its efficacy. The most
common kind of testing is done on animals. The compounds that are eventually put on
the clinical trials are those that are considered appropriate at this point. Additional
adverse effects and human doses may be discovered throughout the clinical trials
[10,11,12]
.
b) Molecular Viewers and Editors:
The three-dimensional structures of biological macromolecules like proteins as well
as tiny molecules may be seen using molecular viewers and editors [13].

MOE

MOLECULAR VIEWERS & EDITORS

SYBYL-X

Accelrys Discovery
Studio

ICM Pro

PyMOL

Chem3D

Chimera

Jmol

Fig. 3. Flow Chart Representation of Molecular Viewers & Editors

1. Accelrys Discovery Studio:

Biovia's software suite Accelrys Discovery Studio is designed to simulate systems of
small and large molecules, including silico methods like molecular mechanics, free
energy calculations, and biotherapeutics advancements. It is a useful instrument for
investigating atomic-level biological and physical-chemical processes. In addition to
maximising biochemical potency, a researcher must simultaneously maximise
additional attributes including toxicity and ADME. It is a sophisticated tool for
protein chemistry, helping with everything from target identification to lead
optimisation to the discovery of small and big molecule medicines. It is an essential
component of molecular analysis and design. Additionally, it comes with a graphical
visualisation tool for sharing, evaluating, and studying data related to models and
proteins [14,15,16,17].
2. Chimera:
The next-generation molecular visualisation programme from the Resource for
Biocomputing, visualisation, and Informatics (RBVI) is called UCSF ChimeraX, or
 just ChimeraX. It comes after UCSF Chimaera. An interactive tool for visualising and
analysing molecular structures and associated data, such as density maps, trajectories,
and sequence alignments, is called UCSF Chimaera. Both free (non-commercial) and
paid versions are accessible [18,19].
3. Chem3D:
Chem 3D is a program that creates vibrant, three-dimensional chemical structures that
are helpful for creating posters, presentations, and medication designs. A two-
dimensional structure may be transformed into a three-dimensional structure using it.
It has the ability to convert CIF images into PDB files. Calculating bond lengths and
angles, doing calculations for molecular modelling, and performing calculations for
molecular dynamics are also helpful [20,21].
4. ICM Pro:
A biologist or chemist can benefit from ICM-Pro's high-quality desktop software
environment for protein structure research, modelling, and docking. Direct access to
structural and sequence databases will be available for all drug design and
development-related tasks. Protein Structure Analysis, Pocket Finder, 3D Interactive
Editor, Protein-Protein Docking, Small Molecule Docking, Protein Structure
Prediction, Mutation Effect Prediction, Bioinformatics Tools, Electrostatics, and
Molecular Graphical Tools are some of its primary features [22,23,24].
5. Jmol:
It is an open-source, free program for writing three-dimensional chemical structures
that is used in drug design. It runs on Linux/Unix, iOS, and Windows, making it
cross-platform. One development toolkit that may be included into other Java apps is
the Jmol Viewer. It works with Firefox, Safari, Chrome, Opera, and Edge, the five
most popular web browsers. The benefit is high-performance 3D rendering without
any hardware requirements [25,26].
6. Molecular Operating Environment (MOE):
One of the computer-based software tools for drug design and cheminformatics is
called MOE. With its extensive, adaptable, and superior modelling tools, MOE excels.
These tools include cheminformatics, statistical data analysis tools, and applications
for protein modelling. It offers a wide range of functions, including protein,
DNA/RNA modelling, virtual screening, antibody design, QSAR, structural
bioinformatics, structure-based drug design, molecular simulations, peptide
 modelling, Structure-Activity Relationship (SAR) Explorer, and three-dimensional
molecular visualisation [27,28].
7. PyMOL:
Schrodinger is the creator and distributor of PyMOL, an open-source molecular
visualisation system. It works with any operating system, including Linux, iOS, and
Windows. The most recent version of PyMOL for this is 2.5 [13].
8. SYBYL-X:
This all-inclusive collection of molecular modelling and simulation tools was created
to speed up drug design and other molecular discovery initiatives, ranging from late
lead optimisation to high throughput screening. SYBYL-X 2.1, the most recent
version, has a new Job Control System that offers a unified interface for the whole
tool set. With the use of this capability, users may submit their work remotely to any
Linux machine that has SYBYL-X installed from Windows, Linux, or Mac.
Additionally, it offers enhanced multi-processor support for important apps including
UNITY, Topomer Search, Surflex-Sim, and Surflex-Dock. Since independent Python
scripts have also been included, QSAR capability may be accessed outside of
SYBYL-X thanks to a Python framework for 3D-QSAR [22,23].

c) Chemical Drawing and Visualization Software:

PubChem sketcher Flare

ChemSketch Ligand Scout

VISUALIZATION SOFTWARE

VISUALIZATION SOFTWARE

Chemdraw ChemBioDraw
CHEMICAL DRAWING &

CHEMICAL DRAWING &

Chemdoodle ChemAxon

Marvin Suite ForgeV10

BKChem Vortex

MedChem
Designer Molinspiration

Activity Miner Accord for Excel

Fig. 4. Flow Chart Representation of Chemical Drawing & Visualization Software

1. Activity Miner:
Key activity changes are highlighted while complicated SAR may be navigated quickl
y with Flare's Activity Miner component.
To improve comprehension, specialised interfaces allow for in-depth examination of a
ctivity cliffs and nearby neighbours.
It can use 3D or 2D connections to compare specific molecules for variations in electr
ostatics, shape, protein interactions, or clusters.
Activity Miner provides an explanation of an activity change's causes.
Finding important chemical pairings in SAR is made easier with its array of data displ
ays.
Activity Miner builds a knowledge of how the electrostatic and shape characteristics c
hange for each pair, which helps in the construction of new compounds with superior
attributes.
The user may concentrate on different facets of SAR because to the multiple perspecti
ves [16,29].
2. Accord for Excel:
Each and every synthetic chemist at Biovitrum uses Accord for Excel, which is an inv
aluable tool.
In order to give chemists (both medicinal and combinatorial) a simple way to compile
and organise structural and analytical data
which is frequently generated from instruments in Excel format—we first purchased
Accord with the combinatorial chemistry add-on.
It gives us a practical way to transfer chemical structures and data between systems an
d work with those structures to do basic computations [30,31].
3. BKChem:
This chemical sketching software is free. Beda Kosata was the one who
conceptualised and wrote it, and Reinis Danne is in charge of keeping it updated.
Python, an outstanding interpreted programming language, is used to write BKChem,
suggesting some of the program's features:
• Platform independence: It functions on any Python-compatible platform.
• Performance: Since Python is an interpreted language, its performance cannot be
expected to match that of a built native code program (a cheap compromise for
 platform independence these days). It uses GNU/Linux for development. Nonetheless,
it was utilised with success in both MacOS X and Windows XP [13].
4. ChemSketch:
A sketching program called ChemSketch makes it possible to depict chemical
structures, such as polymers, organics, organometallics, and Markush structures. In
addition, it offers functions for naming structures (less than fifty atoms and three
rings), cleaning and viewing of 2D and 3D structures, molecular weight, density, and
molar refractivity calculations, as well as logP prediction. Not every feature of the
commercial ChemSketch edition is available in the freeware version. To find out
more about the commercial version, go to ACD/ChemSketch [32,33].
5. Chemdraw:
KingDraw is a free chemical drawing editor that lets users design organic chemistry
objects, processes, and molecules. It also allows users to see 3D models, assess
compound properties, and translate chemical structures into IUPAC designations.
Strong software support for chemical research will be offered by KingDraw, which
will enable quick transitions from KingDraw to Office, ChemDraw, and image.
Additional chemistry-related features and new structural drawing modes will be
available, as well as additional connectivity options between Android & iOS devices
and PC. Numerous potent features are included, including AI picture recognition,
intelligent gesture sketching, structure cleanup, obtaining a 3D model, name-to-
structure conversion, structural formula finding, chemical property analysis,
integrated group, and free sharing [14,34].
6. Chemdoodle;
A two-dimensional molecular sketching application for Unix operating systems is
called XDrawChem. It is comparable to other applications for sketching molecules,
such ChemDraw (TM, CambridgeSoft). It can generate pictures in widely used
formats like PNG and EPS and read and write MDL Molfiles as well as ChemDraw
text and binary files to enable sharing between XDrawChem and other chemistry
apps. Linux, SGI IRIX 6.5, Sun Solaris, Mac OS X, and Windows have all been tried
with XDrawChem [35,36].
7. ChemBioDraw:
ChemDraw, a program offered by CambridgeSoft, has long been the go-to tool for cre
ating chemical structures for illustrations suitable for publishing.
It has also been utilised as the drawing program for electronic notes and database quer
 ies.
Improvements including NMR spectra prediction, TLC plate tools, estimates of molec
ular and physicochemical properties, and structure naming have been added to the soft
ware.
The name change for the most recent version (Version 11) may come as a surprise bec
ause it now emphasises the biological drawing capabilities of BioDraw
more than before [37,38].
8. ChemAxon:
It offers a number of desktop tools, including the drawing program Marvin and add-
ons for calculating different physicochemical characteristics.
An instrument for determining pKa and the corresponding LogD, which is a crucial p
hysicochemical characteristic in medicinal chemistry.
These computations have command-line counterparts that are quite helpful when wor
king with large datasets; a script to examine fragment collections made advantage of t
hese [39,40].
9. Flare:
Research chemists may find new small compounds more quickly and effectively on a
single platform using Flare Viewer, a free version of Flare's ligand- and structure-
based drug discovery solution.
It is employed in the design and ligand binding optimisation process [41,42].
10. ForgeV10:
With ForgeV10, scientists may align, score, and compare various molecules using Cre
sset's unique electrostatic and physicochemical fields.
With the help of the template, the user may create field-based pharmacophores to com
prehend structure-activity relationships and then utilise the virtual screen to find new s
caffolds [43,44].
11. Ligand Scout:
Ligand Scout is a program that uses structural data of macromolecule–ligand complex
es to generate three-dimensional (3D) pharmacophore models.
It includes 3D chemical characteristics that characterise the interaction between a bou
nd small organic molecule (ligand) and the surrounding binding site of the macromole
cule, such as hydrogen bond donors, acceptors, lipophilic regions, and positively and
negatively ionisable chemical groups. Using a pattern-
matching based alignment technique that only takes into account pharmacophoric feat
 ure points rather than chemical structure, these pharmacophores may be stacked and o
verlapped.
In drug design, the program has been successful in predicting novel lead structures
[45,46]
.
12. Marvin Suite:
The Marvin suite is a desktop toolkit with chemical intelligence that facilitates the
drawing, editing, publishing, rendering, importing, and exporting of chemical
structures, as well as the conversion of different chemical and graphical file formats.
For personal, scholarly, and non-commercial usage, it is free. With its many
capabilities, MarvinSketch makes it possible to quickly and precisely sketch chemical
compounds, processes, Markush structures, and query molecules. For both single and
many 2D/3D chemical structures, queries, reactions, and related data, MarvinView is
a powerful chemical viewer. Additionally, it supports the largest range of chemical
file formats that are widely accepted as industry standards [47,48].
13. MedChem Designer:
It is a tool that combines our best-ranked ADMET Predictor's quick and accurate AD
MET property predictions with cutting-edge molecular sketching features.
Chemists who create novel compounds for use in food, pharmaceutical, cosmetic, and
industrial chemical applications will find the extremely user-friendly interface to be q
uite helpful, including a number of convenient features and capabilities that are not fo
und in other molecular sketching software [24].
14. Molinspiration:
A wide range of cheminformatics server tools are available from Molinspiration to su
pport the manipulation and processing of molecules. These tools include the conversio
n of SMILES and SD files, the normalisation of molecules, the creation of tautomers,
the fragmentation of molecules, the computation of different molecular properties req
uired for QSAR, the modelling and drug design of molecules, high
quality molecule depictions, and molecular database tools that support substructure an
d similarity searches.
Additionally supported by our solutions are data visualisation, bioactivity prediction,
and fragment-based virtual screening. The Java-
written Molinspiration tools are compatible for all computer platforms [49,50].
15. PubChem sketcher:
 It is a molecular drawing tool that is network-based and integrated with PubChem. It
is an online repository of data about chemical and biological activities. It is an
interactive drawing tool for chemical structure sketching that is based on the Web. It
is a comprehensive platform for autonomous and validated operation on all major
browsers, including those that are outdated and do not support Web 2. There are zero
JavaScript objects [51,52].

d) Biological Activity Prediction Tools:

Way2Drug

PASS
BIOLOGICAL ACTIVITY
PREDICTION TOOLS

GUSAR

BRENDA

Pharma Expert
Software

Chemical Checker

Toxtree

Fig. 5. Flow Chart Representation of Biological Activity Prediction Tools

1. BRENDA:
It is the most complete information repository on enzymes and enzyme ligand data.
The BRENDA enzyme information system has matured into an extensive system of e
nzyme and enzymeligand information acquired from many sources, linked with flexib
le query methods and assessment tools [53,54].
2. Chemical Checker:
It is a source of tiny molecule commonalities between biology and chemistry. A
variety of drug discovery-related perspectives are used to compare molecules, ranging
from their chemical characteristics to their clinical results [55,56].
3. GUSAR:
 The GUSAR program was designed to generate QSAR/QSPR models using the releva
nt training sets, which are stored as SD files and contain quantitative information on e
ndpoints and chemical structures.
The latest developments in QSAR modelling, such as consensus prediction, applicabil
ity domain assessment, validation of internal and external models, and accurate interp
retations of obtained results, are included in GUSAR, which was developed in accord
ance with OECD (Organisation for Economic Co-operation and Development) princip
les [57,58].
4. PASS:
To characterise the characteristics of chemicals that are biologically active, the biologi
cal activity spectrum was first proposed.
Prediction of activity spectra for substances, or PASS, is a software program that uses
a substance's structural formula to predict over 300 pharmacological effects and bioch
emical mechanisms. It can be effectively used to identify new targets (mechanisms) fo
r specific ligands and, in the opposite direction, to identify new ligands for specific bi
ological targets.
We have created an online user interface (WWW) for the PASS program.
A World Wide Web server has been developed to estimate biological activity spectra o
f drugs online [59,60].
5. Pharma Expert Software:
Each biologically active compound reveals various biological actions in biological sys
tems (human organisms, animals, in vivo and in vitro assays). Since it is not possible t
o study every compound in all currently available tests, the ability to select compound
s with required types of biological activity and without unwanted adverse effects and t
oxicity is highly desirable. The current version of PharmaExpert covers 1587 mechani
sms of action, 418 pharmaco-therapeutical effects, and 2664 types of relationships bet
ween them [61,62].
6. Toxtree:
Toxtree is a feature-rich, adaptable, and user-friendly open-source program that uses a
decision tree method to estimate toxic dangers.
Toxtree may be used with datasets from several kinds of suitable files.
Additionally supported are user-defined chemical structures, which may be input usin
g the integrated 2D structure diagram editor or SMILES [63,64].
7. Way2Drug:
 For about thirty years, a diverse team of researchers with backgrounds in
cheminformatics, bioinformatics, and computer-aided drug development has created
and maintained the Way2Drug portal. It offers a local correspondence theory that
states that the molecular recognition between specific ligand and target atoms
underlies the biological action of drug-like organic substances. Based on this idea, we
have created a consistent set of atom-centered neighbourhoods of atoms descriptors,
which we have applied in various SAR/QSAR/QSPR modelling methodologies.
These descriptors include MNA (Filimonov et al., 1999), QNA (Filimonov et al.,
2009), and LMNA (Rudik et al., 2014) [65,66].

e) Open Source Chemoinformatics Toolkits:

Software development kits known as Open-Source Cheminformatics Toolkits enable
the creation of original computer programs for bioinformatics and virtual screening.
ADMET predictor, MedChem studio, MedChem designer, and OpenBabel are among
the toolkits [13].
Table. 1. Overview of few applications of docking software.

S.No. Software Release Open Operating

Year Access System

1. Molecular Operating 1997 Yes Windows

Environment (MОE)

2. SYBYL-X 2005 Yes Windows

3. Accelrys Discovery Studio 2005 No Windows

4. IСM Pro 1985 No Windows

5. PyMOL 2000 Yes Windows

6. Chimera 2004 Yes Windows

7. Jmol 2000 No Windows

8. PubChem sketcher 2007 Yes Windows

9. ChemSketch 1992 No Windows

10. Сhemdrаw 1985 No Windows

 11. Сhemdооdle 2008 No Windows

12. Mаrvin Suite 2000 No Windows

13. BKСhem 2007 Yes Windows

14. MedСhem Designer 2013 No Windows

15. Activity Miner 2018 Yes Windows

16. Flare 2019 Yes Windows

17. Ligаnd Sсоut 2005 No Windows

18. СhemBiоDrаw 1986 No Windows

19. СhemАxоn 2001 No Windows

20. FоrgeV10 2010 No Windows

21. Vortex 2005 No Windows

22. Mоlinsрirаtiоn 2001 No Windows

23. Ассоrd for Excel 2004 No Windows

24. Wаy2Drug 2013 No Windows

25. РАSS 1997 No Windows

26. GUSAR 2003 No Windows

27. BRENDA 1999 Yes Windows

28. Pharma Expert Software 2004 No Windows

29. Chemical Checker 2008 No Windows

30. Toxtree 2005 Yes Windows

REFERENCES:

1. Teresa K. A, David J. P. S. “Introduction to Bioinformatics”. Genet. Res., Camb.,

1999; 74(2):201-202.
2. Mohamed A. R, Sara A. R, Eslam M. S, Amr S. M. and Nagwa A. S. “Advances in the
Applications of Bioinformatics and Chemoinformatics, Pharmaceuticals”. 2023;
16(7): 1050.
3. Dan E. K, Michael L. R. “Fundamental Concepts in Bioinformatics”. Benjamin
Cummings, 2002: 314.
4. Wishart D.S. “Introduction to Cheminformatics”. Curr. Protoc. Bioinform., 2007:
18, 14.1.1–14.1.21.
5. Yan X. C, Sanders J. M, Gao Y. D, Tudor M, Haidle A. M, Klein D. J, Converso A,
Lesburg C. A, Zang Y, Wood H. B. “Augmenting Hit Identification by Virtual
Screening Techniques in Small Molecule Drug Discovery”. J. Chem. Inf. Model,
2020; 60, 4144–4152.
6. Walters W. P. “Virtual Chemical Libraries”. J. Med. Chem., 2019; 62, 1116–1124.
7. Bhalerao S, Verma D, Rohan L. D, Teli N, Vinodkumar S. D. “Chemoinformatics:
The Application of Informatics Methods to Solve Chemical Problems”. Res. J. Pharm.
Biol. Chem. Sci., 2013; 4, 475.
8. Arthur M. L. “Introduction to Bioinformatics”. Biotech. J., 2008; 3(11):1452-1453.
9. Rakesh R, Saket V. “Dynamics of Bioinformatics In the Artificial Designing of
Drugs”. J. of Global Biosciences. 2019; 8(4), 6137-6145.
10. Banegas L. A. J, Ceron C. J. P, Perez S. H. “A Review of Ligand-based Virtual
Screening Web Tools and Screening Algorithms in Large Molecular Databases in The
Age of Big Data”. Future Med. Chem., 2018;10(22):2641–58.
11. Lin X, Li X, Lin X. “A Review on Applications of Computational Methods in Drug
Screening and Design”. Molecules, 2020; 18;25(6):1375.
12. Patel J. R, Joshi H. V, Shah U. A, Patel J. K. “A Review on Computational Software
Tools for Drug Design and Discovery”. Indo Global J. of Pharm. Sciences, 2022;
12:53–81.
13. Namitha K. N, Velmurugan V. “ Review of Bioinfomatic Tools used in Computer
Aided Drug Design (CADD)”. World J. of Adv. Res. And Rev., 2022; 14(02): 453-
465.
14. Haider M, Chauhan A, Tariq S, Pathak D. P, Siddiqui N, Ali S. “Applications of In
silico Methods in the Design of Drugs for Neurodegenerative Diseases”. Current
Topics in Med. Chem., 2021; 21(11):995–1011.
15. Behl et al. - 2021 - Bioinformatics Accelerates the Major Tetrad A Rea.pdf.
16. Leelananda S. P, Lindert S. “Computational Methods in Drug Discovery”. Beilstein J.
Org. Chem., 2016; 12:2694-718.
17. Rajkishan T, Rachana A, Shruti S, Bhumi P, Patel D. “Computer-Aided Drug
Designing. In: Advances in Bioinformatics”. Springer, 2021; 151-82.
18. Bisht D, Arya R. K. K, Pal G. R, Singh R. P. “A Review on Recent Rational
Approaches to Drug Design, Development and Its Discovery”. Int. J. Life Sci.
Pharma. Res., 2020; 10(4): 96-108.
19. Palaniammal K, Mani M. S. R, Kumar R. M. “Advancing Computer-Aided Drug
Discovery (ACADD): In-Silico Approach towards Nuclear Receptors by Big Data”. J.
of Pharma. Res. Int., 2021; 33(30A): 40-46.
20. Fs A. “Bioinformatics, Genomics, and Proteomics Tools in Drug Design”. J. Drug
Res. Dev. [Internet]. 2019 [cited 2022 Feb 9];5(1).
21. Ghazwani M. Y, Bakheit A. H, Hakami A. R, Alkahtani H. M, Almehizia A. A.
“Virtual Screening and Molecular Docking Studies for Discovery of Potential RNA-
Dependent RNA Polymerase Inhibitors”. Crystals. 2021; 22,11(5):471.
22. Lalita P, Jadon G, Kishor A, Bhadauria R. “A Review on Computer Aided
Drug Design”. 2019.
23. Chandershekar A, Bhaskar A, Mekkanti M. R, Rinku M. “A Review on Computer
Aided Drug Design (CADD) and it's Implications in Drug Discovery and
Development Process”. Int. J. of Health Care and Biological Sciences, 2020; 27-33.
24. Tiwari A, Singh S. “Computational Approaches in Drug Designing. In:
Bioinformatics”. Elsevier, 2022; 207-17.
25. Zhao L, Ciallella H. L, Aleksunes L. M, Zhu H. “Advancing Computer-Aided Drug
Discovery (CADD) by Big Data and Data-Driven Machine Learning Modelling”.
Drug Disc. Today, 2020;25(9):1624–38.
26. Behl T, Kaur I, Sehgal A, Singh S, Bhatia S, Al-Harrasi A. “Bioinformatics
Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry”. IJMS.
2021; 8;22(12):6184.
27. Achary P. G. “Applications of Quantitative Structure-Activity Relationships (QSAR)
Based Virtual Screening in Drug Design: A Review”. Mini Rev. in Med. Chem.,
2020;20(14):1375–88.
28. Willems H, De Cesco S, Svensson F. “Computational Chemistry on a Budget:
Supporting Drug Discovery with Limited Resources: Miniperspective”. J. Med.
Chem., 2020; 24;63(18):10158–69.
29. Ray B, Panigrahi A. K, Dutta S, Gochayat M. “Computer Aided Drug Design: Tools
To Develop Drug For Covid 19”. Asian Journal of Advances in Medical Science.
2021;127–46.
30. Brogi S, Teodorico C. R, Kamil K, Jose L. M. F, Marian V. “Editorial In silico
Methods for Drug Design and Discovery”. Front. Chem., 2020; 8:612.
31. Bharath E. N, Manjula S. N, Vijaychand A. “In Silico Drug Design-Tool For
Overcoming The Innovation Deficit In The Drug Discovery Process”. 2011; 3(2):5.
32. Gurung A. B, Ali M. A, Lee J, Farah M. A, Al-Anazi K. “ An Updated Review of
Computer-Aided Drug Design and Its Application to COVID-19”. Biomed Res Int.
2021; 885-3056.
33. Tutone M, Almerico A. M. “Computational Approaches: Drug Discovery and Design
in Medicinal Chemistry and Bioinformatics”. Molecules, 2021; 11;26(24):7500.
34. Xia X. “Bioinformatics and Drug Discovery”. CTMC, 2017; 26;17(15):1709–26.
35. Mathur M. “Bioinformatics challenges: a review. Bioinformatics”. 2018; 3(6).
36. Rentzsch P, Witten D, Cooper G. M, Shendure J, Kircher M. “CADD: predicting the
deleteriousness of variants throughout the human genome”. NucleicAacids Res.,
2019; 47(D1): 886–94.
37. Mohamed K, Yazdanpanah N, Saghazadeh A, Rezaei N. “Computational drug
discovery and repurposing for the treatment of COVID-19: A systematic review”.
Bioorganic Chem., 2021; 106:104490.
38. Mohamed K, Yazdanpanah N, Saghazadeh A, Rezaei N. “Computational drug
discovery and repurposing for treatment of covid-19”. Elsevier. 2021; 106.
39. Bisht N, Singh B. K. “Role Of Computer Aided Drug Design In Drug Development
And Drug Discovery”. Int. J. of Pharma. Sciences and Res., 2022; 9:11.
40. Jamkhande P. G, Ghante M. H, Ajgunde B. R. “Software based approaches for drug
designing and development: A systematic review on commonly used software and its
applications”. Bulletin of Faculty of Pharmacy, 2017;55(2):203–10.
41. Sabe V. T, Ntombela T, Jhamba L. A, Maguire G. E. M, Govender T, Naicker T.
“Current trends in computer aided drug design and a highlight of drugs discovered via
computational techniques: A review”. Eur. J. Med. Chem., 2021; 15;224:113705.
42. Sauton N, Lagorce D, Villoutreix B. O, Miteva M.A. “MS-DOCK: Accurate multiple
conformation generator and rigid docking protocol for multi-step virtual ligand
screening”. BMC Bioinformatics. 2008; 9(1):184.
43. Brogi S, Ramalho T. C, Kuca K, Medina-Franco J. L, Valko M. “In silico methods for
drug design and discovery”. Frontiers In Chem., 2020; 8:612.
44. Zhou Y, Lauschke V. M. “Computational tools to assess the functional consequences
of rare and noncoding pharmacogenetic variability. Clinical Pharmacology &
Therapeutics”. 2021; 110(3):626–36.
45. Maqsood M, Karim Y, Fatima E, Marriam S, Afzal R. “Computer Aided Drug
Designing (CADD): Tools used for structure-based drug designing”. Biomedical
Letters. 202; 6(2): 149-163.
46. Chukwudozie O. S, Duru V .C, Ndiribe C .C, Aborode A. T, Oyebanji V. O, Emikpe
B. O. “The Relevance of Bioinformatics Applications in the Discovery of Vaccine
Candidates and Potential Drugs for COVID-19 Treatment”. Bioinform. Biol. Insights.
2021; 15:117793222110021.
47. Sarma H, Upadhyaya M, Gogoi B, Phukan M, Kashyap P, Das B. “Cardiovascular
Drugs: an Insight of In Silico Drug Design Tools”. J. of Pharma. Innovation. 2021;1–
26.
48. Baldi A. “Computational approaches for drug design and discovery: An overview”.
Syst. Rev. Pharm. 2010; 1(1):99.
49. Mitjans F, Fernando M. G. “Evaluation of the effects of Climate Change on Air
Transmission Lines, using PLS-CADD Software tools and Hierarchical Analytical
Processes (AHP)”. Case: Paraguay. energy. 202; 11(25):26.
50. Suat S. “Molecular Modelling and Computer Aided Drug Design: The Skill Set Every
Scientist in Drug Research Needs and Can Easily Get”. Hacettepe University J. of the
Faculty of Pharmacy. 2020;40(1):34–47.
51. Hoque I, Chatterjee A, Bhattacharya S, Biswas R. “An Approach of Computer-Aided
Drug Design (CADD) Tools for In Silico Pharmaceutical Drug Design and
Development”. 2017;12.
52. Swain S.S, Rout S .S, Sahoo A, Oyedemi S. O, Hussain T. “Antituberculosis,
antioxidant and cytotoxicity profiles of quercetin: a systematic and cost-effective in
silico and in vitro approach”. Natural Product Research. 2021;1–5.
53. de Esch I. J, Erlanson D. A, Jahnke W, Johnson C. "Fragment-to-Lead Medicinal
Chemistry Publications in 2020”. J. of Med. Chem. 2021; 65(1):84–99.
54. Janvi Gajipara and Georrge. “Tools for ligand based drug discovery”. Recent Trends
in Science and Technology. 2018; 57-64.
55. Surabhi S, Singh B. “Computer aided drug design: an overview”. J. Drug Delivery
Ther. 2018; 18;8(5):504–9.
56. Sauton N, Lagorce D, Villoutreix B. O, Miteva M. A. “MS-DOCK Accurate multiple
conformation generator & rigid docking protocol for multi-step virtual ligand
screening”. BMC Bioinformatics. 2008; 9:184.
57. Venkatachalam C. M, Jiang X, Oldfield T, Waldman M. “Ligand Fit: a novel method
for the shape-directed rapid docking of ligands to protein active sites”. J. of Mol.
Graphics and Modelling. 2003;21(4):289–307.
58. Andricopulo A, Salum L, Abraham D. “Structure-Based Drug Design Strategies in
Medicinal Chemistry’. CTMC. 2009; 9(9):771–90.
59. Bisht N, Sah AN, Bisht S, Joshi H. “Emerging need of today: significant utilization of
various databases and softwares in drug design and development”. Mini Rev. in Med.
Chem. 2021; 21(8):1025–32.
60. Maia E. H.B, Assis L.C, De Oliveira T.A, Da Silva A.M, Taranto A.G. “Structure-
based virtual screening: from classical to artificial intelligence”. Frontiers In
Chemistry. 2020; 8:343.
61. Medina-Franco J. L, Martinez M. K, Fernández-de G. E, Kirchmair J, Bajorath J.
“Rationality over fashion and hype in drug design”. F1000 Res. 2021;10.
62. Schneider P, Walters W. P, Plowright A.T, Sieroka N, Listgarten J, Goodnow R.A.
“Rethinking drug design in the artificial intelligence era”. Nat. Rev. Drug Discov.
2020; 19(5):353–64.
63. Szarecka A, Dobson C. “Protein Structure Analysis: Introducing Students to Rational
Drug Design”. The American Biology Teacher. 2019; 81(6):423–9.
64. Vyas V. “Virtual Screening: A Fast Tool for Drug Design”. Sci Pharm. 2008;
76(3):333–60
65. Zhou S. F, Zhong W. Z. “Drug Design and Discovery: Principles and Applications”.
Molecules. 2017; 22(2):279.
66. Brogi S, Ramalho T. C, Kuca K, Medina F. J. L, Valko M. “Editorial: In silico
Methods for Drug Design and Discovery”. Front. Chem. 2020; 7;8:612.
67. Chukwudozie O, Duru V, Ndiribe C, Oyebanji V. “The Relevance of Bioinformatics
Applications in the Discovery of Vaccine Candidates and Pontential Drugs for Covid-
19”. Bioinformatics and Biology Insights. 2021; 15:1-8.