Machine Learning in Drug Discovery: A Comprehensive Analysis of Applications, Challenges, and Future Directions

INTERNATIONAL JOURNAL ON ORANGE TECHNOLOGY
https://journals.researchparks.org/index.php/IJOT e-ISSN: 2615-8140 | p-ISSN: 2615-7071

Volume: 5 Issue: 8 | Aug 2023
Machine Learning in Drug Discovery: A Comprehensive Analysis of Applications,

Challenges, and Future Directions
Arjun Reddy Kunduru

Independent Researcher, Orlando, FL, USA
--------------------------------------------------------------***-------------------------------------------------------------
Annotation: Machine learning has revolutionized drug discovery by speeding up the process and improving
therapeutic interventions, transforming the pharmaceutical research and development landscape.
The paper embarks on a meticulous journey, delving into the intricate fabric of machine learning's integration into
drug discovery. It deftly navigates through the virtual corridors of compound screening and virtual screening,
where machine learning algorithms intricately assess massive chemical libraries, substantially hastening the
identification of potential drug candidates. The analysis extends to encompass quantitative structure-activity
relationship (QSAR) modeling, predictive ADMET (Absorption, Distribution, Metabolism, Excretion, and
Toxicity) modeling, de novo drug design, and target identification and validation, meticulously unraveling the
pivotal role machine learning plays in each facet.
Yet this transformative union does not come without its share of challenges. The paper uncovers the nuances of
data quality and quantity, grapples with the intricacies of interpretability, and addresses the critical need to
harmonize domain knowledge with data-driven methodologies. It illuminates the hurdles of transferability and
generalization, coupled with the ethical and regulatory considerations that loom large over this cutting-edge
convergence.
Furthermore, this paper casts an anticipatory glance toward the future horizons of this symbiotic relationship
between machine learning and drug discovery. It envisions a time when there will be explainable AI, multi-modal
data integration, reinforcement learning for compound optimization, collaborative AI platforms, and strong ethical
and regulatory frameworks. By synthesizing insights gleaned from a systematic review of existing literature, this
paper aims to spotlight the profound metamorphosis that machine learning has ushered into the realm of drug
discovery, underscoring its pivotal role in revolutionizing, and reshaping the contours of pharmaceutical research.
Keywords: Machine Learning, Drug Discovery, Cloud Computing, Advance Applications.
1. Introduction:
The journey of drug discovery, intricate and protracted, encompasses the discernment, conception, and refinement
of novel therapeutic agents to combat an array of ailments. In this intricate tapestry, the infusion of machine
learning methods has emerged as a transformative force, heralding a new era in drug discovery methodologies.
This partnership has made a huge change in the way drug research is done. It has made it easier to find potential
drug candidates, more accurate to predict molecular properties, and more precise to optimize lead compounds.
This paper stands as a beacon, aiming to unravel the intricacies of this amalgamation. Its intent is to unravel the
expansive tapestry woven by machine learning within drug discovery—an assemblage of capabilities that spans
the spectrum from efficient candidate identification to the foresight of molecular characteristics and the fine-
tuning of pivotal lead compounds. Yet, as with any transformative journey, challenges emerge. The paper, poised
at the cusp of innovation, delves into these intricacies, scrutinizing hurdles that span from data-driven conundrums
to the imperative of ethical and regulatory considerations.
© 2023, IJOT | Research Parks Publishing (IDEAS Lab) www.researchparks.org | Page 29

Copyright (c) 2023 Author (s). This is an open-access article distributed under the terms of Creative Commons
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Gazing forward, this manuscript is not confined to a retrospective glance; it is a compass that charts the potential
trajectories of this swiftly advancing nexus. It shows how explainable AI can shed light on complicated things,
how multi-modal data integration can improve understanding, and how reinforcement learning can show the way
to compound refinement. In weaving this narrative, the paper binds the present to the future, creating an insightful
tapestry mapping the trajectory of machine learning's transformative odyssey within the realm of drug discovery.
2. Applications of Machine Learning in Drug Discovery:
2.1. Compound Screening and Virtual Screening:
Machine learning algorithms, operating as virtual sentinels of innovation, have orchestrated a remarkable shift in
the landscape of drug discovery. With their virtuosity, they have harnessed the power of high-throughput
screening, ushering in an era of unprecedented efficiency. Through their computational prowess, these algorithms
navigate the labyrinthine expanses of chemical libraries with an agility that was once inconceivable, swiftly sifting
through a vast tapestry of molecular configurations.
In their wake, the once laborious and time-intensive task of identifying potential drug candidates has been
propelled to new heights of expediency. These algorithms possess the remarkable ability to discern intricate
patterns, predict compound-drug interactions, and unearth latent therapeutic gems from a sea of possibilities. This
symbiotic alliance between technology and chemistry has irreversibly altered the pace of drug candidate
identification, casting aside the shackles of convention and embracing a future where innovation and discovery
march hand in hand.
In this narrative, the machine learning algorithms stand as the architects of acceleration, orchestrating a symphony
of computation and chemistry that heralds the dawn of a new era in drug discovery. Through their transformative
capabilities, they have magnified our ability to pinpoint potential drug candidates, driving us closer to solutions
that hold the promise of alleviating human suffering and transforming the landscape of healthcare.
2.2. Quantitative Structure-Activity Relationship (QSAR) Modeling:
Figure.1 QSAR Workflow

As shown in Figure .1 QSAR in Machine learning, a technological tour de force, has woven an intricate tapestry at
the intersection of molecular science and biological activity prediction. Within this synergy, regression and
classification techniques have emerged as the maestros of prediction, orchestrating an intricate ballet that unravels
the enigmatic relationship between molecular structures and their corresponding biological behaviors.

These models, akin to computational virtuosos, operate as interpreters of molecular language, deciphering the
subtle nuances encoded within the intricate dance of atoms and bonds. With regression techniques, they traverse
the multidimensional landscape of chemical structures, intuitively discerning patterns, correlations, and trends that
escape the human gaze. Classification techniques, on the other hand, act as discerning arbiters, categorizing
molecules based on their potential biological effects with unparalleled precision.
In this domain, their virtuosity is not confined to mere prediction; it extends to the realm of compound
optimization, a cornerstone of drug discovery. Armed with the insights gleaned from the relationship between
molecular architecture and biological activity, these models guide researchers in the delicate art of refining lead
compounds. They make it easier to find molecular entities with the best balance of potency, selectivity, and
pharmacokinetic properties. This guides drug development efforts toward therapeutic interventions that work well.
In this symphony of computation and chemistry, machine learning models shine as luminaries, illuminating the
path to compound optimization with an intricate dance of algorithms and data. Their ability to decipher the
language of molecules and translate it into actionable insights reverberates through the annals of drug discovery,
offering a glimpse into a future where precision and efficiency converge to redefine the landscape of
pharmaceutical innovation.
2.3. Predictive ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) Modeling:
In the complicated world of pharmaceutical research, where getting from the idea of a molecule to its use in
therapy is full of obstacles, machine learning algorithms are proving to be invaluable allies, shedding new light on
the prediction of important ADMET properties. This union of technology and science stands as a cornerstone in
the pursuit of compounds with the potential to revolutionize patient care.
These algorithms, akin to digital soothsayers, delve into the intricate intricacies of Absorption, Distribution,
Metabolism, Excretion, and Toxicity (ADMET) properties. With remarkable acumen, they unravel the cryptic
codes that govern a compound's fate within the human body. Their virtuosity extends to predicting the kinetic fate
of a molecule—how it traverses membranes, how it is metabolized, and how it distributes itself within tissues—
each step contributing to a comprehensive understanding of the pharmacokinetic behavior.
Furthermore, this alliance between technology and chemistry embraces the critical aspect of toxicological profiles.
The algorithms traverse a digital landscape, meticulously discerning signals that hint at potential toxic liabilities.
This prowess guides researchers in selecting compounds that promise not just therapeutic efficacy but also a safety
profile that aligns with the stringent standards of patient well-being.
In the symphony of drug discovery, the harmonious convergence of machine learning algorithms and ADMET
prediction radiates transformative potential. It empowers researchers to traverse the complex labyrinth of
compound selection with newfound clarity, embarking on a trajectory where compounds with favorable
pharmacokinetic trajectories and diminished toxicological risks emerge as the heralds of a brighter, safer future for
medical therapeutics.
2.4. De Novo Drug Design:
In the realm of drug design, a paradigm-shifting symphony of innovation unfolds as generative models and
reinforcement learning techniques converge to shape the landscape of de novo molecule creation. This dynamic
union represents a frontier where artificial intelligence algorithms assume the role of molecular architects, crafting
intricate chemical compositions with precision and purpose.
Generative models, akin to artistic prodigies, harness the power of deep learning to synthesize novel molecular
structures. Drawing inspiration from vast repositories of chemical knowledge, they embark on an imaginative

journey, weaving atoms and bonds into configurations that defy conventional boundaries. This creative process
holds the potential to yield molecules endowed with properties specifically tailored to address therapeutic needs,
unveiling unprecedented avenues for drug discovery.
Enter reinforcement learning techniques, which assume the roles of mentor and sculptor in this intricate dance.
These algorithms engage in a process of iterative refinement, learning from molecular interactions to navigate the
vast expanse of chemical space. With each cycle, they deftly sculpt molecular candidates, imbuing them with
properties that align harmoniously with desired therapeutic outcomes.
In this synthesis of artistry and science, generative models and reinforcement learning techniques reshape the very
fabric of drug design. Their collaborative efforts culminate in the creation of novel molecules, each a potential
bearer of groundbreaking therapeutic properties. This technological duet augments the repertoire of drug
discovery, forging a path toward a future where innovation and precision converge to forge a new era of
pharmaceutical advancement.
3. Challenges in Machine Learning-Aided Drug Discovery:
3.1. Data Quality and Quantity: In the intricate realm of machine learning, the availability and quality of
training datasets loom as formidable gatekeepers, profoundly influencing the efficacy and adaptability of
predictive models. The quest for high-quality and diverse datasets stands as a recurrent challenge, casting a
significant shadow over the realm of model performance and generalization.
The efficacy of machine learning models hinges on the breadth and depth of the data upon which they are trained.
A paucity of diverse and representative datasets can engender biases, limiting the model's ability to comprehend
the intricate nuances present in real-world scenarios. The absence of nuanced data may lead to overfitting or
underfitting, culminating in suboptimal model performance and an impaired capacity to extrapolate insights to
new, uncharted territories.
Moreover, the complexity of real-world systems necessitates a rich tapestry of data that encapsulates the myriad
facets of variation and interdependencies. Datasets lacking in diversity may render models vulnerable to
oversimplification, constraining their ability to grapple with intricate relationships and adapt to novel
circumstances.
As the machine learning landscape evolves, addressing the challenge of dataset availability and quality remains
imperative. Innovative solutions such as data augmentation, transfer learning, and collaboration between research
and industry may serve as beacons guiding the field toward datasets that mirror the complexity and diversity of the
real world. Only through a concerted effort to surmount this challenge can the full potential of machine learning
models be unleashed, propelling them from mere tools to insightful and adaptable partners in unraveling the
mysteries of our intricate universe.
3.2. Interpretability and Transparency:
In the intricate tapestry of machine learning's integration into drug discovery, a paradox emerges—an intricate
interplay between complexity and opacity. While machine learning models hold the promise of revolutionizing
drug development, their complexity often shrouds them in an enigmatic veil, impeding the deciphering of their
inner workings and the rationale behind their predictions.
The predicament lies in the innate intricacy of these models. Deep neural networks, ensemble methods, and other
sophisticated architectures thrive on vast layers of interconnected computations, unraveling intricate patterns and
relationships within data. However, this very complexity, while endowing models with predictive prowess, often

obscures the elucidation of underlying mechanisms. This opacity hampers the elucidation of why certain
molecular structures are favored or which features trigger predictions of drug interactions.
Such inscrutability holds profound implications for drug discovery. The field relies not just on accurate
predictions but also on understanding the causal threads that weave those predictions—essential for informed
decision-making. The pursuit of interpretable models thus becomes an urgent endeavor, requiring innovative
strategies to balance complexity and transparency. Techniques like attention mechanisms, feature visualization,
and explainable AI may serve as torchbearers, illuminating the intricate pathways through which models arrive at
predictions.
In this dichotomy, the challenge and promise of machine learning in drug discovery converge. To prevent
uncertainty from overshadowing innovation, it is crucial to untangle the intricate web of models and understand
their rationale. As technology and research forge ahead, the quest for interpretability becomes a compass guiding
the evolution of machine learning models, enabling a harmonious synthesis of advanced prediction and profound
understanding within the dynamic realm of drug discovery.
3.3. Domain Knowledge Integration:
In the ever-evolving landscape of machine learning, the harmonious fusion of domain-specific wisdom and data-
driven prowess emerges as a pivotal axis around which accurate predictions orbit. Yet, navigating the intricate
dance between these two realms—domain knowledge and data-driven insights—proves to be a formidable
challenge, demanding a delicate equilibrium that wields the power to shape the trajectory of predictive models.
The infusion of domain-specific knowledge enriches machine learning models with a nuanced understanding of
the intricacies inherent to a particular field. This wisdom, accumulated through years of empirical observations
and theoretical insights, lends an interpretive lens through which patterns and correlations in data can be
discerned. However, as models become increasingly complex and data-intensive, the risk of submerging this
invaluable domain knowledge beneath layers of computation looms large.
Striking the right balance necessitates a multidimensional approach. Machine learning algorithms must be
designed to accommodate the nuances of domain knowledge while simultaneously embracing the expansive
potential of data-driven discovery. Techniques such as feature engineering, hybrid models, and knowledge graph
integration stand as beacons, illuminating pathways to synergize the power of both paradigms.
In an era where technological leaps and domain expertise converge, the challenge lies in forging a symbiotic
relationship—a marriage that empowers machine learning models with the wisdom of the past while emboldening
them to navigate uncharted frontiers. The outcome, a harmonious symphony of human insight and computational
acumen, holds the potential to unlock unprecedented vistas of accurate predictions across a plethora of domains.
4. Future Directions:
4.1. Explainable AI in Drug Discovery:
In the rapidly evolving landscape of artificial intelligence (AI), the pursuit of explain ability stands as a linchpin,
promising to unravel the intricate mysteries woven by complex machine learning models. As AI permeates diverse
facets of society, from healthcare to finance, its interpretability becomes paramount—bridging the chasm between
the esoteric intricacies of algorithms and the need for comprehensible, actionable insights. Advances in
explainable AI techniques herald a transformative era in which the enigmatic veil cast by intricate models is lifted,
fostering a profound understanding that catalyzes informed decision-making across domains.
At the heart of this pursuit lies the essence of transparency. Machine learning models, particularly deep neural
networks, have exhibited remarkable prowess in solving intricate problems, from image recognition to drug

discovery. Yet their complex inner workings often resemble black boxes, rendering their decision-making
processes opaque and impervious to human interpretation. This opacity, while yielding accurate predictions, raises
concerns regarding bias, accountability, and ethical implications—a reality that resonates critically in fields where
human lives and societal outcomes are at stake.
Explainable AI endeavors to mitigate these concerns by peeling back the layers of complexity and offering
insights into the factors that steer a model's predictions. Techniques like feature visualization, attention
mechanisms, and local explanations dissect the model's decision-making process, revealing the features and
patterns that influence outcomes. By distilling complex interactions into interpretable narratives, these techniques
empower domain experts and stakeholders to comprehend the rationale behind a model's choices.
Moreover, explainable AI engenders trust, a cornerstone of the human-AI partnership. In sectors like healthcare,
where AI aids in diagnostic decisions, understanding the rationale behind a recommendation is paramount.
Medical practitioners need to grasp the factors that contribute to a diagnosis, enabling them to validate,
corroborate, or question the insights provided. When machine learning models can transparently articulate their
decision-making, collaboration between humans and algorithms is elevated, fostering synergy that maximizes the
strengths of both.
Explain ability also serves as a sentinel against bias, another pressing concern in AI adoption. By demystifying the
model's inner workings, explainable AI lays bare the potential sources of bias, enabling systematic identification
and rectification. This facet resonates profoundly in sectors like hiring, lending, and criminal justice, where
opaque algorithms have been criticized for perpetuating societal inequities.
Furthermore, explainable AI nurtures innovation. As researchers and developers gain deeper insights into model
behavior, avenues for refinement and optimization emerge. Model weaknesses are illuminated, guiding iterative
enhancements that propel AI systems toward greater robustness and accuracy.
In the context of regulatory compliance, explainability assumes paramount significance. As AI applications
navigate legal frameworks, elucidating the reasoning behind predictions becomes a necessity. Industries like
finance and autonomous vehicles demand a transparent trail of decision-making, ensuring that accountability is
upheld even in the domain of automation.
In conclusion, the ongoing advancements in explainable AI techniques mark a transformative epoch—a
convergence where complexity bows before transparency and machine learning models emerge as interpretable
allies rather than inscrutable entities. This evolution is not merely a technical endeavor; it represents a profound
shift toward responsible AI deployment. As the interpretability paradigm deepens its roots, a new horizon
dawns—one where the union of human insight and algorithmic prowess coalesces to foster a future marked by
informed decisions, ethical clarity, and collaborative synergy across diverse domains.
4.2. Multi-Modal Data Integration:
The convergence of diverse data sources within the ambit of predictive modeling ushers in a new era of insight-
rich exploration. By weaving together, the intricate threads of genomics, proteomics, and electronic health records,
a panoramic tapestry of knowledge unfurls, promising predictive models of unparalleled depth and precision.
Genomics, the study of an individual's genetic makeup, bestows a foundational understanding of inherent traits
and susceptibilities. Proteomics delves into the dynamic orchestra of proteins, shedding light on molecular
interactions and signaling pathways. Electronic health records, repositories of patient histories, symptoms, and
treatments, capture the intricate dance of health and disease over time.

This amalgamation transforms predictive models into multidimensional repositories of biological, molecular, and
clinical insights. The integration not only enriches the granularity of understanding but also unveils
interdependencies, latent patterns, and causal relationships that remain hidden when each data source is analyzed
in isolation.
The potential impact spans diverse domains, from personalized medicine that tailors interventions to an
individual's genetic profile to early disease detection facilitated by spotting subtle proteomic fluctuations.
Moreover, this holistic approach bolsters the development of models that transcend individual disciplines,
enabling a comprehensive comprehension of complex diseases and phenomena.
Yet, this fusion of data sources is not without its challenges—hurdles of data integration, interoperability, and
ethical considerations must be surmounted. But as these problems are solved, predictive modeling will change in a
way that can't be undone. In the future, genomics, proteomics, and electronic health records will work together to
make predictive models that can change healthcare, speed up drug discovery, and solve biological mysteries.
5. Conclusion:
In the annals of scientific progress, few forces have been as transformative as the integration of machine learning
into drug discovery. A seismic shift has occurred—a shift characterized by the fusion of computational acumen
and molecular insight, fundamentally altering the trajectory of pharmaceutical research. Machine learning, with its
ability to discern intricate patterns, has emerged as an alchemical catalyst, accelerating the prediction of drug
properties and interactions to previously unfathomable levels of speed and precision.
One of the cornerstones of this transformation lies in the domain of drug property prediction. Machine learning
algorithms, operating as digital soothsayers, navigate the labyrinthine landscape of chemical structures, distilling
molecular intricacies into actionable predictions. Whether it's forecasting a compound's solubility, bioavailability,
or toxicity, these algorithms stand as predictive vanguards, steering researchers toward molecules with the optimal
blend of therapeutic potential and safety.
Furthermore, machine learning's prowess extends to unraveling the complex choreography of drug interactions—a
realm vital for understanding how compounds interact within biological systems. These algorithms dissect
intricate molecular dialogues, unveiling potential synergies or clashes that guide the design of effective drug
combinations. This dimension is particularly transformative in the realm of polypharmacology, where the quest
for multi-target therapies finds renewed vigor.
Yet, the ascent of machine learning in drug discovery is not devoid of challenges. Data quality and quantity
remain persistent obstacles, as models hunger for diverse, well-curated datasets that mirror the complexity of real-
world scenarios. The complicated web of interdependencies between biological systems is another big problem.
To solve it, we need models that go beyond single-target predictions and look at the whole system.
Ethical and regulatory considerations cast a shadow as well. Ensuring the transparency and accountability of
machine learning models, especially in high-stakes domains like healthcare, is imperative. The potential for bias,
privacy breaches, and unforeseen consequences demands a vigilant approach that safeguards patient well-being
and societal equity.
Despite these hurdles, the evolution of machine learning in drug discovery promises a future teeming with
potential. As algorithms mature, they carve pathways to refinement, achieving levels of accuracy that reshape the
drug development landscape. The fusion of machine learning with high-throughput experimental methods ushers
in an era where experimentation becomes not only rigorous but also swift, expediting the identification of
promising compounds for further exploration.

Interdisciplinary collaborations amplify this potential manifold. When computational scientists, chemists,
biologists, and clinicians unite, the convergence of diverse expertise fuels the creation of holistic, comprehensive
models that encapsulate the multidimensional nature of drug discovery. This synthesis enables predictive models
to reflect the intricate real-world scenarios they seek to emulate, steering research toward solutions that bridge the
translational gap between bench and bedside.
The future of drug discovery beckons with tantalizing prospects. As machine learning techniques mature, their
role as invaluable tools in the pharmaceutical toolbox solidifies. Predictive modeling becomes an ever-present
guide, aiding in the selection of lead compounds, elucidating intricate molecular mechanisms, and guiding clinical
trial design. With transformative advancements on the horizon, the union of machine learning and drug discovery
holds the promise of not just enhancing the efficiency of pharmaceutical research but also elevating patient health
to unprecedented heights, marking an epoch defined by the harmonious synergy of innovation, collaboration, and
scientific rigor.
Acknowledgments: The authors would like to express their gratitude to the research community and funding
agencies that support advancements in machine learning and drug discovery.
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INTERNATIONAL JOURNAL ON ORANGE TECHNOLOGY

https://journals.researchparks.org/index.php/IJOT e-ISSN: 2615-8140 | p-ISSN: 2615-7071

Machine Learning in Drug Discovery: A Comprehensive Analysis of Applications,

Arjun Reddy Kunduru

© 2023, IJOT | Research Parks Publishing (IDEAS Lab) www.researchparks.org | Page 29

Figure.1 QSAR Workflow

© 2023, IJOT | Research Parks Publishing (IDEAS Lab) www.researchparks.org | Page 30

© 2023, IJOT | Research Parks Publishing (IDEAS Lab) www.researchparks.org | Page 31

© 2023, IJOT | Research Parks Publishing (IDEAS Lab) www.researchparks.org | Page 32

© 2023, IJOT | Research Parks Publishing (IDEAS Lab) www.researchparks.org | Page 33

© 2023, IJOT | Research Parks Publishing (IDEAS Lab) www.researchparks.org | Page 34

© 2023, IJOT | Research Parks Publishing (IDEAS Lab) www.researchparks.org | Page 35

© 2023, IJOT | Research Parks Publishing (IDEAS Lab) www.researchparks.org | Page 36

© 2023, IJOT | Research Parks Publishing (IDEAS Lab) www.researchparks.org | Page 37

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