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Koam ANA, Majeed MU, Zaman S, Ahmad A, Masmali I, Ahmadini AAH. Machine learning approaches for modeling the physiochemical characteristics of polycyclic aromatic hydrocarbons. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2025; 48:21. [PMID: 40317407 DOI: 10.1140/epje/s10189-025-00487-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2024] [Accepted: 04/01/2025] [Indexed: 05/07/2025]
Abstract
Supervised machine learning methods like random forests and extreme gradient boosting plays an important role in drug development for predicting bioactivity and resolving structure-activity correlations. These approaches use topological descriptors in the study of polycyclic aromatic hydrocarbons that represent molecular structural characteristics to enhance the prediction capacity of quantitative structure-property relationships (QSPR). The objective is to identify the physoichemical properties such as density, boiling point, flash point, enthalpy, polarizability, surface tension, molar volume, molecular weight and complexity that significantly impact physicochemical attributes. The combination of machine learning and QSPR also demonstrates the potential of computational techniques in drug development. Then effective algorithms are constructed to express the link between the eccentricity-based topological indices and the physicochemical characteristics of each of the polycyclic aromatic hydrocarbons, which grows our understanding of their behavior and paves the way for future development of environmental forecasting techniques and toxicological evaluations of polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Ali N A Koam
- Department of Mathematics, College of Science, Jazan University, P.O. Box: 114, 45142, Jazan, Kingdom of Saudi Arabia
| | | | - Shahid Zaman
- Department of Mathematical and Physical Sciences, College of Arts and Sciences, University of Nizwa, 616, Nizwa, Sultanate of Oman
| | - Ali Ahmad
- Department of Computer Science, College of Engineering and Computer Science, Jazan University, Jazan, Kingdom of Saudi Arabia.
| | - Ibtisam Masmali
- Department of Mathematics, College of Science, Jazan University, P.O. Box: 114, 45142, Jazan, Kingdom of Saudi Arabia
| | - Abdullah Ali H Ahmadini
- Department of Mathematics, College of Science, Jazan University, P.O. Box: 114, 45142, Jazan, Kingdom of Saudi Arabia
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Zaman S, Ahmed W, Siddiqui MK, Mumtaz A, Kosar Z. Role of eccentricity based topological descriptors to predict anti-HIV drugs attributes with supervised machine learning algorithms. Comput Biol Med 2025; 190:110101. [PMID: 40154201 DOI: 10.1016/j.compbiomed.2025.110101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Revised: 03/23/2025] [Accepted: 03/25/2025] [Indexed: 04/01/2025]
Abstract
Chemical graphs are mathematical representations of molecular structures, where atoms are represented as vertices, while chemical bonds are depicted as edges of a graph. The chemical graphs are widely used in cheminformatics to analyze molecular properties, predict biological activity and design new drugs. A topological index (TI) in drug design is a numerical descriptor of a molecular graph that correlates its structure with biological activity and physicochemical properties. The aim of this study is to use the concepts of chemical graphs to examine the molecular characteristics and structural design of anti-HIV drugs. Secondly, we have utilized the concept of supervised machine learning to create a predictive model. Finally, we have compared the results of different machine learning algorithms such as Random Forest algorithm and XGBoost algorithm. These methods not only enhance drug effectiveness but also aid in predicting new drug candidates.
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Affiliation(s)
- Shahid Zaman
- Department of Mathematical and Physical Sciences, College of Arts and Sciences, University of Nizwa, 616, Nizwa, Sultanate of Oman.
| | - Wakeel Ahmed
- Department of Mathematics, COMSATS University Islamabad, Lahore Campus, Pakistan; Department of Mathematics, University of Sialkot, Sialkot, 51310, Pakistan.
| | | | - Aqsa Mumtaz
- Department of Mathematics, University of Sialkot, Sialkot, 51310, Pakistan.
| | - Zunaira Kosar
- Department of Mathematics, University of Sargodha, Sargodha, 40100, Pakistan.
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Subashini G, Kannan K, Menaga A. Exponential Wiener index of some silicate networks. Sci Rep 2024; 14:27214. [PMID: 39516254 PMCID: PMC11549481 DOI: 10.1038/s41598-024-77771-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 10/25/2024] [Indexed: 11/16/2024] Open
Abstract
Any graph that depicts a particular molecular structure can be given a topological graph index, also known as a molecular descriptor. This index can be used to examine numerical data and discover more about specific physical properties of molecules. Silicates are hard crystals that can be sliced into little pieces. Therefore, silicon play a vital role in many real time applications. It is the authentic material to make microchips which run in PDA, PC and other game tools. In the current study, we have determined the new topological index for a few silicate structures, including cyclic, single-chain, and Pyro silicates by grouping the vertices of the corresponding molecular graphs based on their distance sums. This index is known as the exponential Wiener index. It is expanded to include their line graphs as well. The numerical values of exponential Wiener index and multiplicative exponential Wiener index for the molecular graphs of cyclic silicates, single chain silicates and their line graphs with n vertices where n = 3, 4, 5 are explored.
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Affiliation(s)
- G Subashini
- Department of Mathematics, Srinivasa Ramanujan Centre, SASTRA Deemed to be University, Kumbakonam, Tamil Nadu, 612001 , India
| | - K Kannan
- Department of Mathematics, Srinivasa Ramanujan Centre, SASTRA Deemed to be University, Kumbakonam, Tamil Nadu, 612001 , India.
| | - A Menaga
- Department of Computer Science and Engineering, Srinivasa Ramanujan Centre, SASTRA Deemed to be University, Kumbakonam, Tamil Nadu, 612001 , India
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Khan AR, Bhatti SA, Tawfiq F, Siddiqui MK, Hussain S, Ali MA. On degree-based operators and topological descriptors of molecular graphs and their applications to QSPR analysis of carbon derivatives. Sci Rep 2024; 14:21543. [PMID: 39278960 PMCID: PMC11403011 DOI: 10.1038/s41598-024-72621-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 09/09/2024] [Indexed: 09/18/2024] Open
Abstract
This work initiates a concept of reduced reverse degree basedRR D M -Polynomial for a graph, and differential and integral operators by using thisRR D M -Polynomial. In this study twelve reduced reverse degree-based topological descriptors are formulated using theRR D M -Polynomial. The topological descriptors, denoted as T D 's, are numerical invariants that offer significant insights into the molecular topology of a molecular graph. These descriptors are essential for conducting QSPR investigations and accurately estimating physicochemical attributes. The structural and algebraic characteristics of the graphene and graphdiyne are studied to apply this methodology. The study involves the analysis and estimation of Reduced reverse degree-based topological descriptors and physicochemical features of graphene derivatives using best-fit quadratic regression models. This work opens up new directions for scientists and researchers to pursue, taking them into new fields of study.
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Affiliation(s)
- Abdul Rauf Khan
- Department of Mathematics, Faculty of Sciences, Ghazi University, Dera Ghazi Khan, 32200, Pakistan
| | - Saad Amin Bhatti
- Department of Mathematics, Faculty of Sciences, Ghazi University, Dera Ghazi Khan, 32200, Pakistan
| | - Ferdous Tawfiq
- Mathematics Department, College of Science, King Saud University, P.O. Box 22452, Riyadh, 11495, Saudi Arabia
| | | | - Shahid Hussain
- Energy Engineering Division, Department of Engineering Science and Mathematics, Lulea University of Technology, Lulea, Sweden
| | - Mustafa Ahmed Ali
- Department of Mathematics, Faculty of Science, Somali National University, Mogadishu, Somalia.
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Ahmed W, Zaman S, Asif E, Ali K, Mahmoud EE, Asheboss MA. Exploring the role of topological descriptors to predict physicochemical properties of anti-HIV drugs by using supervised machine learning algorithms. BMC Chem 2024; 18:167. [PMID: 39267184 PMCID: PMC11395299 DOI: 10.1186/s13065-024-01266-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 08/12/2024] [Indexed: 09/14/2024] Open
Abstract
In order to explore the role of topological indices for predicting physio-chemical properties of anti-HIV drugs, this research uses python program-based algorithms to compute topological indices as well as machine learning algorithms. Degree-based topological indices are calculated using Python algorithm, providing important information about the structural behavior of drugs that are essential to their anti-HIV effectiveness. Furthermore, machine learning algorithms analyze the physio-chemical properties that correspond to anti-HIV activities, making use of their ability to identify complex trends in large, convoluted datasets. In addition to improving our comprehension of the links between molecular structure and effectiveness, the collaboration between machine learning and QSPR research further highlights the potential of computational approaches in drug discovery. This work reveals the mechanisms underlying anti-HIV effectiveness, which paves the way for the development of more potent anti-HIV drugs. This work reveals the mechanisms underlying anti-HIV efficiency, which paves the way for the development of more potent anti-HIV drugs which demonstrates the invaluable advantages of machine learning in assessing drug properties by clarifying the biological processes underlying anti-HIV behavior, which paves the way for the design and development of more effective anti-HIV drugs.
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Affiliation(s)
- Wakeel Ahmed
- Department of Mathematics, University of Sialkot, Sialkot, 51310, Pakistan.
- Department of Mathematics, COMSATS University, Islamabad Lahore Campus, Lahore, 51000, Pakistan.
| | - Shahid Zaman
- Department of Mathematics, University of Sialkot, Sialkot, 51310, Pakistan
- Department of Mathematical and Physical Sciences, University of Nizwa, Nizwa, Oman
| | - Eizzah Asif
- Department of Mathematics, University of Sialkot, Sialkot, 51310, Pakistan
| | - Kashif Ali
- Department of Mathematics, COMSATS University, Islamabad Lahore Campus, Lahore, 51000, Pakistan
| | - Emad E Mahmoud
- Department of Mathematics and Statistics, Collage of Science, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia
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Yu G, Zaman S, Jabeen M, Zuo X. The study of pentagonal chain with respect to schultz index, modified schultz index, schultz polynomial and modified schultz polynomial. PLoS One 2024; 19:e0304695. [PMID: 38889185 PMCID: PMC11185496 DOI: 10.1371/journal.pone.0304695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
Distance-based topological indices are numerical parameters that are derived from the distances between atoms in a molecular structure, and they provide a quantitative measure of the topology and geometry of a molecule. The distance-based topological indices uses to predict various properties of molecules, including their boiling points, melting points, and solubility. It also predicts the biological activity of molecules, including their pharmacological and toxicological properties. Pentagonal chain molecules are organic compounds that consist of a linear chain of five-membered (pentagons) connected by carbon and bonds. These molecules have unique structural and electronic properties that make them useful in a variety of applications. Motivated by the pentagonal chain molecules, we have considered a pentagonal chain graph and it is denoted by Pn. We have computed some distance based topological indices for Pn. The paper focuses on a pentagonal chain molecules denoted by G, and derives several distance-based topological indices. These indices compromise insights into physicochemical properties, aid in identifying structural characterizations, and enhance understanding of molecular properties.
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Affiliation(s)
- Guofeng Yu
- Public Courses Education Department, Anhui Business Vocational College, Hefei, Anhui, China
| | - Shahid Zaman
- Department of Mathematics, University of Sialkot, Sialkot, Pakistan
| | - Mah Jabeen
- Department of Mathematics, University of Sialkot, Sialkot, Pakistan
| | - Xuewu Zuo
- General Education Department, Anhui Xinhua University, Hefei, China
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Abubakar MS, Aremu KO, Aphane M, Amusa LB. A QSPR analysis of physical properties of antituberculosis drugs using neighbourhood degree-based topological indices and support vector regression. Heliyon 2024; 10:e28260. [PMID: 38571658 PMCID: PMC10987931 DOI: 10.1016/j.heliyon.2024.e28260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/05/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024] Open
Abstract
Topological indices are molecular descriptors used in QSPR modelling to predict the physicochemical properties of molecules. Topological indices are used in numerous applications in drug design. In this work, we compute the neighbourhood degree-based topological indices of 15 antituberculosis drugs, we studied the QSPR analysis of these drugs using support vector regression. The efficiency of support vector regression is determined by comparing it with the classical linear regression. Our QSPR model further shows the superiority of the SVR model as a better predictive model in QSPR analysis of the physical properties of antituberculosis drugs. The findings in this study are a further contribution to the field of chemical graph theory and drug design, providing a deeper understanding of neighbourhood degree-based topological indices and their predictive capabilities in QSPR model.
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Affiliation(s)
- Muhammad Shafii Abubakar
- Department of Mathematics and Applied Mathematics, Sefako Makgatho Health Sciences University, P.O. Box 60, 0204, Pretoria, South Africa
| | - Kazeem Olalekan Aremu
- Department of Mathematics and Applied Mathematics, Sefako Makgatho Health Sciences University, P.O. Box 60, 0204, Pretoria, South Africa
- Department of Mathematics, Usmanu Danfodiyo University Sokoto, P.M.B. 2346, Sokoto State, Nigeria
| | - Maggie Aphane
- Department of Mathematics and Applied Mathematics, Sefako Makgatho Health Sciences University, P.O. Box 60, 0204, Pretoria, South Africa
| | - Lateef Babatunde Amusa
- Department of Statistics, University of Ilorin, P.M.B. 1515, Ilorin, Kwara State, Nigeria
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Zaman S, Hakami KH, Rasheed S, Agama FT. Reduced reverse degree-based topological indices of graphyne and graphdiyne nanoribbons with applications in chemical analysis. Sci Rep 2024; 14:547. [PMID: 38177204 PMCID: PMC10767102 DOI: 10.1038/s41598-023-51112-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/30/2023] [Indexed: 01/06/2024] Open
Abstract
Graphyne and Graphdiyne Nanoribbons reveal significant prospective with diverse applications. In electronics, they propose unique electronic properties for high-performance nanoscale devices, while in catalysis, their excellent surface area and reactivity sort them valuable catalyst supports for numerous chemical reactions, contributing to progresses in sustainable energy and environmental remediation. The topological indices (TIs) are numerical invariants that provide important information about the molecular topology of a given molecular graph. These indices are essential in QSAR/QSPR analysis and play a significant role in predicting various physico-chemical characteristics. In this article, we present a formula for computing reduced reverse (RR) degree-based topological indices for graphyne and graphdiyne nanoribbons, including the RR Zagreb indices, RR hyper-Zagreb indices, RR forgotten index, RR atom bond connectivity index, and RR Geometric-arithmetic index. We also execute a graph-theoretical analysis and comparison to demonstrate the critical significance and validate the acquired results. Our findings provide insights into the structural and chemical properties of these nanoribbons and contribute to the development of new materials for various applications.
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Affiliation(s)
- Shahid Zaman
- Department of Mathematics, University of Sialkot, Sialkot, 51310, Pakistan.
| | - K H Hakami
- Department of Mathematics, Faculty of Science, Jazan University, 45142, Jazan, Saudi Arabia
| | - Sadaf Rasheed
- Department of Mathematics, University of Sialkot, Sialkot, 51310, Pakistan
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