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Journal articles on the topic 'Molecular modeling study'

Author: Grafiati

Published: 6 June 2025

Last updated: 25 July 2025

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1

Chandrasekaran, Rengaswami, Srinivas Janaswamy, and Victor J. Morris. "Acetan:glucomannan interactions—a molecular modeling study." Carbohydrate Research 338, no. 24 (2003): 2889–98. http://dx.doi.org/10.1016/j.carres.2003.08.018.

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2

Bharat Kumar S. Ankalagi, Nagaraj Gangadhar Hanshul, Ramprasad H., et al. "Molecular Modeling." international journal of engineering technology and management sciences 7, no. 3 (2023): 454–58. http://dx.doi.org/10.46647/ijetms.2023.v07i03.60.

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In this paper, the modelling of molecule is presented. Chemistry, as the central science, utilizes models in virtually every aspect of the discipline. Integral to the progress of chemistry has been its ability to draw from physics, mathematics, statistics, and computer science to develop new sub disciplines, such as computational chemistry. As computing hardware has become faster and more accessible, so to have techniques to perform modelling and simulations of molecular systems. Software systems today assist researchers in the study of molecular systems and provide mechanisms for deriving a r

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3

Ayadi, Leila, Damien Forget, Alain Martelli, Jean-François Constant, Martine Demeunynck, and Christian Coulombeau. "Molecular modeling study of DNA abasic sites." Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) 104, no. 3-4 (2000): 284–89. http://dx.doi.org/10.1007/s002140000140.

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4

Gandhi, Neha, Brijesh K. Srivastava, Vidya B. Lohray, and Braj B. Lohray. "Oxazolidine-2-thiones: a molecular modeling study." Tetrahedron Letters 45, no. 33 (2004): 6269–72. http://dx.doi.org/10.1016/j.tetlet.2004.06.090.

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5

COX, M. B., P. ARJUNAN, and S. K. ARORA. "Naphthyridinomycin-DNA adducts: A molecular modeling study." Journal of Antibiotics 44, no. 8 (1991): 885–94. http://dx.doi.org/10.7164/antibiotics.44.885.

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6

P, Srivastava. "Comparative Modeling and Molecular Interaction Study for the Management of AMD and CRVO Ocular Disorder." Open Access Journal of Ophthalmology 8, no. 1 (2023): 1–13. http://dx.doi.org/10.23880/oajo-16000263.

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Age Related Macular Degeneration (AMD) and Central Retinal Vein Occlusion (CRVO) are the rare and leading cause of blindness among patients with ocular problem. Many proteins are reported in the progression of these ocular disorders. Proteins which are directly involved in the development of this disorder reported in the literature, their sequence related information retrieved from biological databases. In silico technique was implemented in order to characterize the properties and structures of the proteins using ProtParam. For studying about the potential phosphorylation sites in protein gen

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7

Soufi, W., M. Merad, F. BOUKLI Hacene, and S. Ghalem. "Study of Monoamine Oxidase-B and Indole Derivatives Using Two Molecular Docking Programs: Molegro and MOE." International Journal of Scientific Research and Management 8, no. 09 (2020): 25–31. http://dx.doi.org/10.18535/ijsrm/v8i09.c01.

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Inhibition of the enzyme Monoamine oxidase (MAO) is an important approach in the treatment of Parkinson’s disease. A series of indole derivatives were synthesised and evaluated as inhibitors of MAO-B may give insight to develop new ways of antiparkinson drug, In general, the derivatives were found to be selective MAO-B inhibitors with IC50 values . MAO-B inhibitors, are considered useful in the therapy of Parkinson’s disease since oxidation by MAO-B represents a major catabolic pathway of dopamine in the central nervous system .  Our goal of research is to study the inhibition of MAO-B b

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8

Martinho, Nuno, Helena Florindo, Liana Silva, Steve Brocchini, Mire Zloh, and Teresa Barata. "Molecular Modeling to Study Dendrimers for Biomedical Applications." Molecules 19, no. 12 (2014): 20424–67. http://dx.doi.org/10.3390/molecules191220424.

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9

Liang, Li, Naijue Zhu, Julian White, Courtney Brown, and Cheryl L. Klein‐Stevensx. "A crystallographic and molecular modeling study of butyrophenones." Journal of Pharmaceutical Sciences 87, no. 12 (1998): 1496–501. http://dx.doi.org/10.1021/js980253e.

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10

Skovstrup, Søren, Signe Grann Hansen, Troels Skrydstrup, and Birgit Schiøtt. "Conformational Flexibility of Chitosan: A Molecular Modeling Study." Biomacromolecules 11, no. 11 (2010): 3196–207. http://dx.doi.org/10.1021/bm100736w.

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11

Alves, C. R., L. J. O. Figueiredo, F. A. L. O. Saraiva, and S. G. De Simone. "Molecular modeling study on a Leishmania cysteine proteinase." Journal of Molecular Structure: THEOCHEM 539, no. 1-3 (2001): 289–95. http://dx.doi.org/10.1016/s0166-1280(00)00799-5.

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12

Lee, Hyun Mee, Jong-Ki Kim, and Seog K. Kim. "Molecular Modeling Study of the Norfloxacin-DNA Complex." Journal of Biomolecular Structure and Dynamics 19, no. 6 (2002): 1083–91. http://dx.doi.org/10.1080/07391102.2002.10506811.

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13

Andzelm, Jan, James Sloan, Eugene Napadensky, Steven Mcknight, and David Rigby. "Molecular modeling study of sulfonated SIBS triblock copolymers." Molecular Simulation 32, no. 2 (2006): 163–72. http://dx.doi.org/10.1080/08927020600728613.

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14

Zhikol, Oleg A., Svitlana V. Shishkina, Victoria V. Lipson, et al. "Low molecular weight supramolecular dehydroepiandrosterone-based gelators: synthesis and molecular modeling study." New Journal of Chemistry 43, no. 33 (2019): 13112–21. http://dx.doi.org/10.1039/c9nj01390c.

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Three novel isomeric low molecular weight dehydroepiandrosterone-based gelators are synthesized. Their ability to self-assemble is studied in several solvents both experimentally and theoretically by molecular modeling.

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15

Manunza, B., S. Deiana, M. Pintore, V. Solinas, and C. Gessa. "A molecular modeling study of the urease active site." Journal of Molecular Structure: THEOCHEM 419, no. 1-3 (1997): 33–36. http://dx.doi.org/10.1016/s0166-1280(97)00245-5.

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16

Dodziuk, Helena, and Grigory Dolgonos. "Molecular modeling study of hydrogen storage in carbon nanotubes." Chemical Physics Letters 356, no. 1-2 (2002): 79–83. http://dx.doi.org/10.1016/s0009-2614(02)00368-8.

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17

Seridi, Lynda, та Ahmed Boufelfel. "Molecular modeling study of Lamotrigine/β-cyclodextrin inclusion complex". Journal of Molecular Liquids 158, № 2 (2011): 151–58. http://dx.doi.org/10.1016/j.molliq.2010.11.011.

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18

Wu, Xiongwu, Peijun Zhang, Cezar M. Khursigara, Sriram Subramaniam, and Bernard R. Brooks. "Electron Tomography and Molecular Modeling Study of Chemoreceptor Organization." Biophysical Journal 98, no. 3 (2010): 383a. http://dx.doi.org/10.1016/j.bpj.2009.12.2064.

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19

Boulanger, Yvan, Abdesslem Khiat, Zhen-Hua Zhou, Gaétan Caron, and Lolita O. Zamir. "NMR and molecular modeling study of paclitaxel putative precursors." Tetrahedron 52, no. 27 (1996): 8957–68. http://dx.doi.org/10.1016/0040-4020(96)00444-9.

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20

Efremov, Roman G., Pavel E. Volynsky, Dmitry E. Nolde, Peter V. Dubovskii, and Alexander S. Arseniev. "Interaction of Cardiotoxins with Membranes: A Molecular Modeling Study." Biophysical Journal 83, no. 1 (2002): 144–53. http://dx.doi.org/10.1016/s0006-3495(02)75156-4.

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21

Gadhe, Changdev G., Gugan Kothandan, Thirumurthy Madhavan, and Seung Joo Cho. "Molecular modeling study of HIV-1 gp120 attachment inhibitors." Medicinal Chemistry Research 21, no. 8 (2011): 1892–904. http://dx.doi.org/10.1007/s00044-011-9711-4.

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22

Tarakanova, Anna, and Markus J. Buehler. "Molecular modeling of protein materials: case study of elastin." Modelling and Simulation in Materials Science and Engineering 21, no. 6 (2013): 063001. http://dx.doi.org/10.1088/0965-0393/21/6/063001.

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23

Rajendran, M., R. Ravichandran, and D. Devapiriam. "Molecular Modeling Study of Quercetin and their Metal Complexes." International Journal of Computer Applications 50, no. 22 (2012): 30–34. http://dx.doi.org/10.5120/7937-1266.

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24

Iwamoto, N. "A property trend study of polybenzimidazole using molecular modeling." Polymer Engineering and Science 34, no. 5 (1994): 434–37. http://dx.doi.org/10.1002/pen.760340509.

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25

Xu, Xiao Ying, Feng Cheng, Jian Hua Shen, et al. "Agonist-PPAR? interactions: Molecular modeling study with docking approach." International Journal of Quantum Chemistry 93, no. 6 (2003): 405–10. http://dx.doi.org/10.1002/qua.10575.

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26

Fülöp, László, and János Ecker. "Modeling of biopolymerases: a simple case study." Journal of Universal Science Online 5, no. 1 (2022): 1–12. http://dx.doi.org/10.17202/juso.2022.5.1.

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We reviewed the new methods that can be used in the recycling of biomass, with regard to the modeling of enzymes and the new possibilities of their application. Progress has been made in the pretreatment of biomass, as well as in the diversity and application of the enzymes used, but based on molecular modeling, very little progress has been made in development. There is also minimal progress in modifying the enzymes used during biomass processing to adapt to environmental conditions. There are hardly any publications where molecular modeling techniques are used to modify, improve, and adapt e

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27

Höltje, Hans-Dieter. "Molecular Modeling Untersuchungen zur Struktur des Barbiturat-Rezeptors. On the Structure of the Barbiturate Receptor: A Molecular Modeling Study." Archiv der Pharmazie 319, no. 6 (1986): 570–72. http://dx.doi.org/10.1002/ardp.19863190617.

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28

Behmard, Esmaeil, Parviz Abdolmaleki, Ebrahim Barzegari Asadabadi, and Samad Jahandideh. "Prevalent Mutations of Human Prion Protein: A Molecular Modeling and Molecular Dynamics Study." Journal of Biomolecular Structure and Dynamics 29, no. 2 (2011): 379–89. http://dx.doi.org/10.1080/07391102.2011.10507392.

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29

Shchodryi, V., D. Lozhko, and Z. Tkachuk. "Molecular docking study of oligonucleotides with D-mannitol." Visnik ukrains'kogo tovaristva genetikiv i selekcioneriv 15, no. 1 (2017): 64–68. http://dx.doi.org/10.7124/visnyk.utgis.15.1.714.

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Aim. Complex of yeast RNA and D-mannitol has a specific antiviral activity. This complex inhibits the neuraminidase and hemagglutinin activity of viruses such as influenza, parainfluenza and thus it blocks virus entry into the cell and his replication. So, nowadays, study of the interaction of this compound is an important task. Study interaction of the oligoribonucleotides and oligodesoxynucleotides with D mannitol molecule. Methods. Molecular modeling structure of oligoribonucleotides and oligodesoxynucleotides were done by using «Hyperchem» software package. The AutoDock program was used to

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30

BAMBA, Kafoumba, Fatogoma DIARRASSOUBA, Mawa KONÉ, Ahissan Donatien EHOUMAN, and Sopi Thomas AFFI. "Design of new electron acceptors based on Tetracyanoquinodimethane (TCNQ) by molecular modeling techniques and Structure-Property Relationship (SPR) study." SDRP Journal of Computational Chemistry & Molecular Modelling 4, no. 1 (2020): 313–20. http://dx.doi.org/10.25177/jccmm.4.1.ra.10599.

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31

Li, Jibin, and Ismael Hidalgo. "Molecular modeling study of structural requirements for the oligopeptide transporter." Journal of Drug Targeting 4, no. 1 (1996): 9–17. http://dx.doi.org/10.3109/10611869609046256.

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32

Zhu, Jing Chuan, Jie Cheng, and Bo Liu. "Self-Assembly Effects of Cyclic Peptide Dimers: Molecular Modeling Study." Key Engineering Materials 353-358 (September 2007): 2257–60. http://dx.doi.org/10.4028/www.scientific.net/kem.353-358.2257.

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The cyclic peptides can self-assemble into β-sheet like antiparallel tubular ensembles through intermolecular hydrogen-bonding interaction. Under the self-assembling effects of the dimer subunits, various aggregate properties may alter with the change of the structure. The relationship between the property and structure of ensembles is extremely important for designing new nanostructures. Molecular mechanics (MM) and molecular dynamics (MD) were employed to investigate the structure and property of single dimer and dimer-ensemble from cyclo-[D-Phe-(1R, 3S)-γ-Acc]3. Results reveal that the sing

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33

Muhammad, Auwal, Kanikar Muangchoo, Ibrahim A. Muhammad, et al. "A molecular modeling study of novel aldose reductase (AR) inhibitors." AIMS Biophysics 7, no. 4 (2020): 380–92. http://dx.doi.org/10.3934/biophy.2020026.

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34

Barbosa, Jardel, João Ferreira, Antonio Figueiredo, et al. "Molecular modeling and chemometric study of anticancer derivatives of artemisinin." Journal of the Serbian Chemical Society 76, no. 9 (2011): 1263–82. http://dx.doi.org/10.2298/jsc111227111b.

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In this work, a molecular modeling and multivariate study involving artemisinin and 28 derivatives with activity against human hepatocellular carcinoma HepG2 is reported. The studied calculations of the compounds were performed at the B3LYP/6-31G level. MEP maps were used in an attempt to identify key structural features of artemisinin and its derivatives that are necessary for their activities, and to investigate their interaction with the transferrin. The chemometrics methods PCA, HCA, KNN, SIMCA and SDA were employed in order to reduce dimensionality and to investigate which subset of varia

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35

Hongju, Wang, Ma Kaiming, Liu Zhonghua, Jin Dongzhu, and Wei Wenqiang. "Molecular modeling and docking study of acetylcholinesterase from Camelus dromedarius." Journal of Camel Practice and Research 23, no. 2 (2016): 241. http://dx.doi.org/10.5958/2277-8934.2016.00041.2.

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36

Aksan, Sinem. "OPTICAL PROPERTIES OF BaTi0,99Sr0,01O3 SOLAR CELLS: A MOLECULAR MODELİNG STUDY." International journal of ecosystems and ecology science (IJEES) 14, no. 3 (2024): 41–48. http://dx.doi.org/10.31407/ijees14.306.

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37

Delfino, Reinaldo T., and José D. Figueroa-Villar. "Nucleophilic Reactivation of Sarin-Inhibited Acetylcholinesterase: A Molecular Modeling Study." Journal of Physical Chemistry B 113, no. 24 (2009): 8402–11. http://dx.doi.org/10.1021/jp810686k.

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38

Montgomery, Craig D. "Mechanisms of Pentacoordinate Pseudorotation. A Molecular Modeling Study of PF5." Journal of Chemical Education 78, no. 6 (2001): 844. http://dx.doi.org/10.1021/ed078p844.

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39

Aksimentiev, A., and K. Schulten. "Extending molecular modeling methodology to study insertion of membrane nanopores." Proceedings of the National Academy of Sciences 101, no. 13 (2004): 4337–38. http://dx.doi.org/10.1073/pnas.0400739101.

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40

Abdelhafez, Omaima M., Kamelia M. Amin, Hamed I. Ali, Timothy J. Maher, and Rasha Z. Batran. "Dopamine release and molecular modeling study of some coumarin derivatives." Neurochemistry International 59, no. 6 (2011): 906–12. http://dx.doi.org/10.1016/j.neuint.2011.08.004.

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41

Zhang, Xiangying, Hongbin Sun, Xiaoan Wen, and Haoliang Yuan. "A Selectivity Study of FFAR4/FFAR1 Agonists by Molecular Modeling." Journal of Chemical Information and Modeling 59, no. 10 (2019): 4467–74. http://dx.doi.org/10.1021/acs.jcim.9b00735.

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42

Panek, Jarosław J., Aneta Jezierska, Krzysztof Mierzwicki, Zdzisław Latajka, and Aleksander Koll. "Molecular Modeling Study of Leflunomide and Its Active Metabolite Analogues." Journal of Chemical Information and Modeling 45, no. 1 (2005): 39–48. http://dx.doi.org/10.1021/ci049754d.

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43

Brandsen, J., J. Kroon, and K. Gubernator. "Stereoselective hydrolysis with rabbit liver esterase: a molecular modeling study." Journal of Molecular Graphics 12, no. 1 (1994): 69. http://dx.doi.org/10.1016/0263-7855(94)80048-0.

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44

Medina-Gonzalez, Yaocihuatl, Ahmed Jarray, Séverine Camy, Jean-Stéphane Condoret, and Vincent Gerbaud. "CO2-Expanded Alkyl Lactates: A Physicochemical and Molecular Modeling Study." Journal of Solution Chemistry 46, no. 2 (2017): 259–80. http://dx.doi.org/10.1007/s10953-016-0565-8.

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45

Miyahara, Minoru, Hideki Kanda, Tomohisa Yoshioka, and Morio Okazaki. "Modeling Capillary Condensation in Cylindrical Nanopores: A Molecular Dynamics Study." Langmuir 16, no. 9 (2000): 4293–99. http://dx.doi.org/10.1021/la991227e.

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46

Chu, Hui-Ying, Qing-Chuan Zheng, Yong-Shan Zhao, and Hong-Xing Zhang. "Homology modeling and molecular dynamics study on N-acetylneuraminate lyase." Journal of Molecular Modeling 15, no. 3 (2008): 323–28. http://dx.doi.org/10.1007/s00894-008-0398-5.

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47

Saugues, Emmanuelle, Lionel Nauton, Vincent Théry, Fabrice Anizon, and Pascale Moreau. "Synthesis and molecular modeling study of new trimeric quinoline derivatives." Bioorganic Chemistry 39, no. 4 (2011): 143–50. http://dx.doi.org/10.1016/j.bioorg.2011.07.001.

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48

Ahmad, Nasir, Aqsa Farman, Syed Lal Badshah, Ata Ur Rahman, Haroon ur Rashid, and Khalid Khan. "Molecular modeling, simulation and docking study of ebola virus glycoprotein." Journal of Molecular Graphics and Modelling 72 (March 2017): 266–71. http://dx.doi.org/10.1016/j.jmgm.2016.12.010.

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49

Edwards, Jesse, Genzo Tanaka, April Anderson, Claudia Eybl, Henry Joung Lee, and Zhengqing You. "Molecular Modeling of Steroid–Nucleoside Conjugates: A Preliminary Structural Study." Structural Chemistry 14, no. 5 (2003): 467–78. http://dx.doi.org/10.1023/b:stuc.0000004491.09786.f4.

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50

XIE, L., and G. FARRINGTON. "Application of molecular modeling to the study of polymer electrolytes." Solid State Ionics 60, no. 1-3 (1993): 19–28. http://dx.doi.org/10.1016/0167-2738(93)90269-9.

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