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Journal articles on the topic 'Molecular docking'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Dias, Raquel, and Walter de Azevedo Jr. "Molecular Docking Algorithms." Current Drug Targets 9, no. 12 (2008): 1040–47. http://dx.doi.org/10.2174/138945008786949432.

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2

Nilesh, More* Deepali Wagh Chaitali Chavan Rutik Lotan Navasare Devesh Himmatsing Rajput. "A Review on Molecular Docking." International Journal of Pharmaceutical Sciences 2, no. 12 (2024): 433–40. https://doi.org/10.5281/zenodo.14274558.

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Molecular docking is a computational approach used to model the structural complexes that arise from the interactions between two or more molecules. Its main goal is to predict the three-dimensional configuration of the target molecule, making it a vital technique in the realm of drug development. The availability of molecular data and structural databases has become increasingly important in this area. Molecular docking provides a range of advanced tools for drug design and analysis, with the straightforward prediction of molecular interactions and easy access to structural databases serving

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3

Sabrina Benouis, Sabrina Benouis, Fouad Ferkous Fouad Ferkous, Khairedine Kraim Khairedine Kraim, Ahmed Allali Ahmed Allali, and Youcef Saihi Youcef Saihi. "Molecular Docking Studies on Gingerol Analogues toward Mushroom Tyrosinase." Journal of the chemical society of pakistan 42, no. 2 (2020): 214. http://dx.doi.org/10.52568/000630.

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The gingerol presents the starting point of our work which aims to discover new inhibitors of the tyrosinase enzyme. Therefore, we have studied the activity of gingerol derivatives as inhibitors against mushroom tyrosinase based on the molecular docking. Molecular docking studies were performed on a series of gingerol analogues retrieved from Zinc database (with 70% as similarity threshold). The gingerol analogues were docked within the active site region of mushroom tyrosinase (PDB: 2Y9X) using Molegro Virtual Docker V.5.0. The results of molecular docking studies revealed that some analogues

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Sabrina Benouis, Sabrina Benouis, Fouad Ferkous Fouad Ferkous, Khairedine Kraim Khairedine Kraim, Ahmed Allali Ahmed Allali, and Youcef Saihi Youcef Saihi. "Molecular Docking Studies on Gingerol Analogues toward Mushroom Tyrosinase." Journal of the chemical society of pakistan 42, no. 2 (2020): 214. http://dx.doi.org/10.52568/000630/jcsp/42.02.2020.

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The gingerol presents the starting point of our work which aims to discover new inhibitors of the tyrosinase enzyme. Therefore, we have studied the activity of gingerol derivatives as inhibitors against mushroom tyrosinase based on the molecular docking. Molecular docking studies were performed on a series of gingerol analogues retrieved from Zinc database (with 70% as similarity threshold). The gingerol analogues were docked within the active site region of mushroom tyrosinase (PDB: 2Y9X) using Molegro Virtual Docker V.5.0. The results of molecular docking studies revealed that some analogues

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5

Berenger, Francois, Ashutosh Kumar, Kam Y. J. Zhang, and Yoshihiro Yamanishi. "Lean-Docking: Exploiting Ligands’ Predicted Docking Scores to Accelerate Molecular Docking." Journal of Chemical Information and Modeling 61, no. 5 (2021): 2341–52. http://dx.doi.org/10.1021/acs.jcim.0c01452.

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6

Elokely, Khaled M., and Robert J. Doerksen. "Docking Challenge: Protein Sampling and Molecular Docking Performance." Journal of Chemical Information and Modeling 53, no. 8 (2013): 1934–45. http://dx.doi.org/10.1021/ci400040d.

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7

Morris, Connor J., and Dennis Della Corte. "Using molecular docking and molecular dynamics to investigate protein-ligand interactions." Modern Physics Letters B 35, no. 08 (2021): 2130002. http://dx.doi.org/10.1142/s0217984921300027.

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Molecular docking and molecular dynamics (MD) are powerful tools used to investigate protein-ligand interactions. Molecular docking programs predict the binding pose and affinity of a protein-ligand complex, while MD can be used to incorporate flexibility into docking calculations and gain further information on the kinetics and stability of the protein-ligand bond. This review covers state-of-the-art methods of using molecular docking and MD to explore protein-ligand interactions, with emphasis on application to drug discovery. We also call for further research on combining common molecular d

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8

Rani, Nidhi, Prerna Sharma, Vikas Kumar Sharma, and Praveen Kumar. "Molecular Docking Approach to Identify Potential AntiCandidal Potential of Curcumin." Journal of Pharmaceutical Technology, Research and Management 8, no. 2 (2020): 67–71. http://dx.doi.org/10.15415/jptrm.2020.82008.

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Background: Candida albicans is a kind of fungus that can lead to mortality. In the presence of the enzyme Lanosterol-demethylase, Ergosterol, the major sterol in the fungal cell membrane, is the resulting product of Lanosterol (Cytochrome P450DM). Purpose: Azole antifungal drugs target this enzyme as a target enzyme. The work included selecting and modelling the target enzyme. Cucumin’s inhibitory effect on Cytochrome P450 was tested utilising molecular docking experiments. Methods: Chem sketch was used to create compound structures, and Molergo Virtual Docker was used to do molecular docking

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9

Tessaro, Francesca, and Leonardo Scapozza. "How ‘Protein-Docking’ Translates into the New Emerging Field of Docking Small Molecules to Nucleic Acids?" Molecules 25, no. 12 (2020): 2749. http://dx.doi.org/10.3390/molecules25122749.

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In this review, we retraced the ‘40-year evolution’ of molecular docking algorithms. Over the course of the years, their development allowed to progress from the so-called ‘rigid-docking’ searching methods to the more sophisticated ‘semi-flexible’ and ‘flexible docking’ algorithms. Together with the advancement of computing architecture and power, molecular docking’s applications also exponentially increased, from a single-ligand binding calculation to large screening and polypharmacology profiles. Recently targeting nucleic acids with small molecules has emerged as a valuable therapeutic stra

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10

Fan, Jiyu, Ailing Fu, and Le Zhang. "Progress in molecular docking." Quantitative Biology 7, no. 2 (2019): 83–89. http://dx.doi.org/10.1007/s40484-019-0172-y.

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11

Guedes, Isabella A., Camila S. de Magalhães, and Laurent E. Dardenne. "Receptor–ligand molecular docking." Biophysical Reviews 6, no. 1 (2013): 75–87. http://dx.doi.org/10.1007/s12551-013-0130-2.

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12

Mitchell, Julie C., Sharokina Shahbaz, and Lynn F. Ten Eyck. "Interfaces in Molecular Docking." Molecular Simulation 30, no. 2-3 (2004): 97–106. http://dx.doi.org/10.1080/0892702031000152217.

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13

Narender, Boggula, Katta Mahaboobi Sruthi, Megavath Subhash, Mukherjee Jayanti, and Rao Tadikonda Rama. "Molecular Docking - An Overview." Chemistry Research Journal 8, no. 5 (2023): 24–34. https://doi.org/10.5281/zenodo.11382179.

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<strong>Abstract </strong> Molecular docking has become an increasingly important tool for drug discovery. In this review, we present a brief introduction of the available molecular docking methods, and their development and applications in drug discovery. Molecular docking has been widely employed as a fast and inexpensive technique in the past decades, both in academic and industrial settings. Although this discipline has now had enough time to consolidate, many aspects remain challenging and there is still not a straightforward and accurate route to readily pinpoint true ligands among a set

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14

Salih, Twana Mohsin. "A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model." Iraqi Journal of Pharmaceutical Sciences ( P-ISSN 1683 - 3597 E-ISSN 2521 - 3512) 31, no. 2 (2022): 160–68. http://dx.doi.org/10.31351/vol31iss2pp160-168.

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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicte

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15

Burle, Sushil S., Krishna R. Gupta, Yogeshri J. Jibhkate, Atul T. Hemke, and Milind J. Umekar. "Insights into molecular docking: A comprehensive view." International Journal of Pharmaceutical Chemistry and Analysis 10, no. 3 (2023): 175–84. http://dx.doi.org/10.18231/j.ijpca.2023.030.

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Molecular docking software is mainly used in drug development. Molecular docking offers a wide range of useful techniques for the creation and analysis of pharmaceuticals. Before now, predicting the target for a receptor was extremely challenging however, docking the target protein with a ligand is a straightforward and dependable procedure presently and binding affinity is designed. To see a molecule's three-dimensional structure, a variety of docking tools have been created. The docking score can also be examined using a variety of computational techniques. This review mainly emphases on the

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16

S., G. Desai, N. M. Gohel Dr., K. D. Parmar Dr., and A. R. Mohapatra Dr. "In-silico Molecular Docking: Shifting Paradigms in Pesticide Discovery." International Journal of Environmental & Agriculture Research (IJOEAR) 10, no. 8 (2024): 01–17. https://doi.org/10.5281/zenodo.13609198.

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In-silico molecular docking has emerged as a transformative tool in pesticide discovery, offering detailed insights into the interactions between small molecules and biological targets. This review explores the foundational aspects of molecular docking, outlining its critical steps, including target selection, ligand preparation, docking simulation, scoring and post-docking analysis. It delves into the various types of molecular docking rigid and flexible. The role of molecular docking in insect pest management is examined, highlighting its effectiveness in identifying novel targets, optimizin

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17

Naji, Amel Mohson, Ahmed Mutanabbi Abdula, Olfat A. Nief, and Ebtihal K. Abdullah. "Synthesis, Characterization, Antimicrobial and Molecular Docking Study of Benzooxadiazole Derivatives." Chemistry & Chemical Technology 16, no. 1 (2022): 25–33. http://dx.doi.org/10.23939/chcht16.01.025.

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In this study, a series of new1,2,5-oxadiazole compounds derived from 4-chloro-7-nitro-benzo 1,2,5-oxadiazole was synthesized using different organic procedures. The resulting derivatives were chemically characterized and their structures were confirmed by FT-IR and NMR analysis. All the compounds were also evaluated for their antibacterial and antifungal activity against four types of pathogenic bacteria: S.aureus, S.epidermidis (as gram-negative bacteria), E.coli, Klebsiella spp. (as gram-positive bacteria) and the fungus Candida albicans using the agar well diffusion method. The synthesized

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18

Chopra, Neetu, Kiranpreet kaur, and Sanjeev Kumar. "Synthesis, Molecular Docking and Antimicrobial Evaluation of New Tetrahydrobenzothienopyrimidine Derivatives." International Journal of Trend in Scientific Research and Development Volume-2, Issue-6 (2018): 1084–96. http://dx.doi.org/10.31142/ijtsrd18756.

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19

Zhu, Tian-Wang, Yu Zheng та Rui-Xin Li. "Screening potential anti-osteoarthritis compounds using molecular docking based on MAPK and NFκB pathways and validating their anti-osteoarthritis effect". PLOS ONE 20, № 3 (2025): e0319686. https://doi.org/10.1371/journal.pone.0319686.

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Osteoarthritis is an extremely common disease. However, it lacks effective nonsurgical treatments. Molecular docking has been widely used in drug discovery. However, no studies focus on screening anti-osteoarthritis compounds using molecular docking. This study aimed to screen potential anti-osteoarthritis compounds using molecular docking and validate their anti-osteoarthritis effect. Molecular dockings between 51 compounds inhibiting the MAPK and NFκB pathways but have not been used to treat osteoarthritis and 5 core human proteins in the MAPK and NFκB pathways were performed. Corilagin, Api

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20

Fan, Mengran, Jian Wang, Huaipan Jiang, et al. "GPU-Accelerated Flexible Molecular Docking." Journal of Physical Chemistry B 125, no. 4 (2021): 1049–60. http://dx.doi.org/10.1021/acs.jpcb.0c09051.

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21

Atkovska, Kalina, Sergey Samsonov, Maciej Paszkowski-Rogacz, and M. Pisabarro. "Multipose Binding in Molecular Docking." International Journal of Molecular Sciences 15, no. 2 (2014): 2622–45. http://dx.doi.org/10.3390/ijms15022622.

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22

Suvannang, Naravut, Chanin Nantasenamat, Chartchalerm Isarankura-Na-Ayudhya, and Virapong Prachayasittikul. "Molecular Docking of Aromatase Inhibitors." Molecules 16, no. 5 (2011): 3597–617. http://dx.doi.org/10.3390/molecules16053597.

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23

Brooijmans, Natasja, and Irwin D. Kuntz. "Molecular Recognition and Docking Algorithms." Annual Review of Biophysics and Biomolecular Structure 32, no. 1 (2003): 335–73. http://dx.doi.org/10.1146/annurev.biophys.32.110601.142532.

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24

Liu, Yu, Lei Zhao, Mingli Li, and Changfei Zhao. "Swarm intelligence for molecular docking." International Journal of Modelling, Identification and Control 18, no. 4 (2013): 357. http://dx.doi.org/10.1504/ijmic.2013.053541.

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25

Bastos, M., M. H. dos Santos, and I. Camps. "Molecular docking vs structure optimization." Journal of Organic Chemistry Research 1, no. 1 (2013): 1–9. http://dx.doi.org/10.12785/jocr/010101.

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26

Huang, Niu, Brian K. Shoichet, and John J. Irwin. "Benchmarking Sets for Molecular Docking." Journal of Medicinal Chemistry 49, no. 23 (2006): 6789–801. http://dx.doi.org/10.1021/jm0608356.

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27

Shoichet, Brian K., Susan L. McGovern, Binqing Wei, and John J. Irwin. "Lead discovery using molecular docking." Current Opinion in Chemical Biology 6, no. 4 (2002): 439–46. http://dx.doi.org/10.1016/s1367-5931(02)00339-3.

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28

Ouh-young, Michael Pique, Mark Harris, John Hughes, Neela Srinivasan, and FrederickP Brooks. "Force display in molecular docking." Journal of Molecular Graphics 6, no. 4 (1988): 224. http://dx.doi.org/10.1016/s0263-7855(98)80039-8.

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29

Salo, Jukka-Pekka, Ari Yliniemelä, and Jyrki Taskinen. "Parameter Refinement for Molecular Docking." Journal of Chemical Information and Computer Sciences 38, no. 5 (1998): 832–39. http://dx.doi.org/10.1021/ci9801825.

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30

Sturlese, Mattia, Massimo Bellanda, and Stefano Moro. "NMR-Assisted Molecular Docking Methodologies." Molecular Informatics 34, no. 8 (2015): 513–25. http://dx.doi.org/10.1002/minf.201500012.

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31

Gschwend, Daniel A., Andrew C. Good, and Irwin D. Kuntz. "Molecular docking towards drug discovery." Journal of Molecular Recognition 9, no. 2 (1996): 175–86. http://dx.doi.org/10.1002/(sici)1099-1352(199603)9:2<175::aid-jmr260>3.0.co;2-d.

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32

Sobolev, Vladimir, Rebecca C. Wade, Gert Vriend, and Marvin Edelman. "Molecular docking using surface complementarity." Proteins: Structure, Function, and Bioinformatics 25, no. 1 (1996): 120–29. http://dx.doi.org/10.1002/(sici)1097-0134(199605)25:1<120::aid-prot10>3.0.co;2-m.

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33

Sobolev, Vladimir, Rebecca C. Wade, Gert Vriend, and Marvin Edelman. "Molecular docking using surface complementarity." Proteins: Structure, Function, and Genetics 25, no. 1 (1996): 120–29. http://dx.doi.org/10.1002/(sici)1097-0134(199605)25:1<120::aid-prot10>3.3.co;2-1.

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34

Shoichet, Brian K., Andrew R. Leach, and Irwin D. Kuntz. "Ligand solvation in molecular docking." Proteins: Structure, Function, and Genetics 34, no. 1 (1999): 4–16. http://dx.doi.org/10.1002/(sici)1097-0134(19990101)34:1<4::aid-prot2>3.0.co;2-6.

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35

Shoichet, Brian K., Irwin D. Kuntz, and Dale L. Bodian. "Molecular docking using shape descriptors." Journal of Computational Chemistry 13, no. 3 (1992): 380–97. http://dx.doi.org/10.1002/jcc.540130311.

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36

Rudnitskaya, Aleksandra, Béla Török, and Marianna Török. "Molecular docking of enzyme inhibitors." Biochemistry and Molecular Biology Education 38, no. 4 (2010): 261–65. http://dx.doi.org/10.1002/bmb.20392.

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37

Kaur, Kiranpreet, Paranjeet Kaur, Amit Mittal, Surendra Kumar Nayak, and Gopal L. Khatik. "DESIGN AND MOLECULAR DOCKING STUDIES OF NOVEL ANTIMICROBIAL PEPTIDES USING AUTODOCK MOLECULAR DOCKING SOFTWARE." Asian Journal of Pharmaceutical and Clinical Research 10, no. 16 (2017): 28. http://dx.doi.org/10.22159/ajpcr.2017.v10s4.21332.

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Objective: Design of novel antimicrobial peptides and study through the molecular docking.Methods: The molecular structures were drawn in ChemBiodraw ultra and by the help of ChemBiodraw 3D, all structures were energy minimized by theMM2 method and converted to pdbextension file which is readable at the ADT interface. The AutoDock Vina (ADT) 1.5.6 software is used for molecular docking purposes.Results: Eight antimicrobial peptides (AMPs) were designed based on theMP196antimicrobial peptide. Among these KP_03R (FWRWRW-NH2) showed good binding affinity. These peptides also showed the stereochem

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38

Anand, S. Athavan Alias, C. Loganathan, K. Saravanan, and S. Kabilan. "Comparison of Molecular Docking and Molecular Dynamics Simulations of 1,3-Thiazin-4-One with MDM2 Protein." International Letters of Chemistry, Physics and Astronomy 60 (September 2015): 161–67. http://dx.doi.org/10.18052/www.scipress.com/ilcpa.60.161.

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The molecular docking and molecular dynamics simulations studies of 1,3–thiazin–4–one derivative with a bonafide oncogene protein MDM2 (PDB ID: 4HBM) was investigated. Both the docking and dynamics simulations were performed in Schrödinger software suite 2014 using Glide and Desmond modules. The results of docking and dynamics were compared to investigate the possible binding modes of the thiazinone derivative with 4HBM. The tested molecule shows critical interactions with the important amino acid His 96 which is necessary for the inhibition of MDM2 in both docking and dynamic studies.

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39

Anand, S. Athavan Alias, C. Loganathan, K. Saravanan, and S. Kabilan. "Comparison of Molecular Docking and Molecular Dynamics Simulations of 1,3-Thiazin-4-One with MDM2 Protein." International Letters of Chemistry, Physics and Astronomy 60 (September 30, 2015): 161–67. http://dx.doi.org/10.56431/p-m93n64.

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The molecular docking and molecular dynamics simulations studies of 1,3–thiazin–4–one derivative with a bonafide oncogene protein MDM2 (PDB ID: 4HBM) was investigated. Both the docking and dynamics simulations were performed in Schrödinger software suite 2014 using Glide and Desmond modules. The results of docking and dynamics were compared to investigate the possible binding modes of the thiazinone derivative with 4HBM. The tested molecule shows critical interactions with the important amino acid His 96 which is necessary for the inhibition of MDM2 in both docking and dynamic studies.

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40

Bastos, Luana Luiza, and Giovana Fiorini. "Re-docking Molecular Utilizando o PyMOL e AutoDock VINA." BIOINFO 3, no. 1 (2023): 21. http://dx.doi.org/10.51780/bioinfo-03-21.

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O tutorial a seguir aborda a técnica de re-docking utilizada como etapa inicial em simulações de docking molecular para validar a ferramenta utilizada, bem como suas funções de pontuação. O re-docking consiste em separar um complexo proteína-ligante resolvido experimentalmente e buscar encontrar uma conformação parecida através do docking. Neste tutorial utilizaremos o PyMOL como uma ferramenta visual auxiliar para o re-docking utilizando o Vina.

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41

Santos, Lorena Limao Vieira dos, Jhonatas Rodrigues Barbosa, Renato Araújo da Costa, and Lourenço Lúcia de Fátima Henriques. "Antimicrobial packaging based on molecular docking of natural products." Peer Review 6, no. 15 (2024): 203–16. http://dx.doi.org/10.53660/prw-2493-4518.

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For a long time, studies on food packaging focused on antimicrobial agents, without, however, explaining the mechanisms. Therefore, in this analysis and opinion text, we approach the promising scenario, regarding the use of molecular docking techniques in the development of antimicrobial packaging. Molecular docking was identified as an important guidance tool, showing researchers which molecules had effective antimicrobial activity and their mechanisms. Furthermore, based on molecular docking studies, researchers were able to optimize in vitro and in vivo antimicrobial experiments. The target

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42

Kay, Mak Kit, Pichika Mallikarjuna Rao, Sandeep Kumar Singh, et al. "Synthesis, Characterization, And Bioactivity Studies Of Triazolothiadiazines As Potential Antifungal Agents." International Journal of Environmental Sciences 11, no. 7s (2025): 411–18. https://doi.org/10.64252/ejh4rc19.

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The escalating issue of antifungal resistance necessitates the development of novel therapeutic agents, particularly those containing azole scaffolds (Synthesis, Antifungal Activities, Molecular Docking and Molecular ..., 2023). This research focuses on the synthesis, comprehensive characterization, and evaluation of the bioactivity of triazolothiadiazine derivatives as promising antifungal candidates (Synthesis, Antifungal Activities, Molecular Docking and Molecular ..., 2023). A series of seventeen novel triazole derivative compounds were synthesized, with their structures rigorously elucida

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43

Jakhar, Ritu, Mehak Dangi, Alka Khichi, and Anil Kumar Chhillar. "Relevance of Molecular Docking Studies in Drug Designing." Current Bioinformatics 15, no. 4 (2020): 270–78. http://dx.doi.org/10.2174/1574893615666191219094216.

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Molecular Docking is used to positioning the computer-generated 3D structure of small ligands into a receptor structure in a variety of orientations, conformations and positions. This method is useful in drug discovery and medicinal chemistry providing insights into molecular recognition. Docking has become an integral part of Computer-Aided Drug Design and Discovery (CADDD). Traditional docking methods suffer from limitations of semi-flexible or static treatment of targets and ligand. Over the last decade, advances in the field of computational, proteomics and genomics have also led to the de

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Gautam, Suman, Shailesh Pathak, and Shwetank H. Dubey. "The Role of Molecular Docking in Modern Drug Discovery and Development: A Comprehensive Review." Journal of Drug Discovery and Health Sciences 1, no. 03 (2024): 129–37. https://doi.org/10.21590/jddhs.01.03.02.

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Molecular docking is an essential computational technique widely used in drug discovery to predict the interaction between small molecules and their protein targets. This review presents a detailed examination of molecular docking, including its historical development and current relevance in pharmaceutical research. It outlines the core principles of molecular docking, differentiating between rigid and flexible docking methods and discussing the critical components such as search algorithms and scoring functions. The review highlights the role of molecular docking in identifying and validatin

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45

Adhilakshmi, A., and S. Darlin Quine. "Design, Molecular Docking, DFT and Antimicrobial Studies of Novel Benzimdazole Derivatives." International Journal of Science and Research (IJSR) 11, no. 1 (2022): 1319–24. http://dx.doi.org/10.21275/sr22121144929.

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46

Das, Paramita, Rahim Bagwan, Syed Sohaila, et al. "Anti-Tuberculosis and Molecular Docking Study of – Rhizomes of Curcuma caesia." Indian Journal Of Science And Technology 16, no. 47 (2024): 4504–11. http://dx.doi.org/10.17485/ijst/v16i47.2996.

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47

Yadav, Khushi Joshi Ankur* Khemani Purva Malviya Sapna Kharia Anil. "A Short Review Docking: Structure Based Drug Design." International Journal of Pharmaceutical Sciences 2, no. 9 (2024): 1013–27. https://doi.org/10.5281/zenodo.13820440.

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Molecular docking plays a vital role in advancing scientific research, particularly in drug development and understanding biomolecular interactions. This computational approach simulates the binding of small molecules, such as potential drugs, to specific biological targets like proteins or DNA. By predicting the optimal binding configuration and energy, molecular docking helps identify promising drug candidates and sheds light on the underlying mechanisms of biological processes. The accuracy of this method relies heavily on a robust scoring function, which distinguishes between strong and we

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48

Deshmukh, Harshada S., Vaishnavi M. Dhangude, Tanvi A. Bhosale,, et al. "Precision in Binding: An Insightful Review on Molecular Docking Techniques and their Applications." South Asian Research Journal of Pharmaceutical Sciences 7, no. 01 (2025): 29–42. https://doi.org/10.36346/sarjps.2025.v07i01.005.

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The numerical modelling of structural compounds made up of two or more interacting molecules is known as molecular docking. Predicting the desired three-dimensional structure is the aim of molecular docking. Software for molecular docking is mostly utilised in drug development. Easy access to structural databases and molecules have become crucial mechanisms. Molecular docking is a potent computer technique that is essential for structural biology, drug development, and bio-molecular interaction research, giving a comprehensive understanding of its significance in contemporary scientific resear

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49

Martis, Elvis A. F., and Stéphane Téletchéa. "Ten quick tips to perform meaningful and reproducible molecular docking calculations." PLOS Computational Biology 21, no. 5 (2025): e1013030. https://doi.org/10.1371/journal.pcbi.1013030.

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Molecular docking is a useful method for predicting the binding affinity and conformation of small chemical entities to support lead optimisation. It is also used to virtually screen a large chemical database to find new chemical entities. There are several docking programs available with different algorithms and varying preparation steps. We identify ten quick tips that apply to molecular docking irrespective of the program one might choose. Our objective is to provide the beginners with important things to keep in mind while using molecular docking for their research. We aim to ensure that e

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50

Sulimov, Alexey, Danil Kutov, Ivan Ilin, and Vladimir Sulimov. "Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations." Nanomaterials 12, no. 2 (2022): 274. http://dx.doi.org/10.3390/nano12020274.

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Abstract:

The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method

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