Relevant bibliographies by topics / Molecular docking

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Molecular docking'

Author: Grafiati
Published: 4 June 2021
Last updated: 25 July 2025

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Journal articles on the topic "Molecular docking"

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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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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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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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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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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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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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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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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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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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Dissertations / Theses on the topic "Molecular docking"

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Iakovou, Georgios. "Simulating molecular docking with haptics." Thesis, University of East Anglia, 2015. https://ueaeprints.uea.ac.uk/59468/.

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Intermolecular binding underlies various metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow the study of the binding process. In molecular docking, haptics enables the user to sense the interaction forces and intervene cognitively in the docking process. Haptics-assisted docking systems provide an immersive virtual docking environment where the user can interact with the molecules, feel the interaction forces using their sense of touch, identify visually
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Atkovska, Kalina, Sergey A. Samsonov, Maciej Paszkowski-Rogacz, and M. Teresa Pisabarro. "Multipose Binding in Molecular Docking." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-147177.

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Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e.,
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Landaverde, Raphael J. "GPU optimizations for a production molecular docking code." Thesis, Boston University, 2014. https://hdl.handle.net/2144/21199.

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Thesis (M.Sc.Eng.) -- Boston University<br>Scientists have always felt the desire to perform computationally intensive tasks that surpass the capabilities of conventional single core computers. As a result of this trend, Graphics Processing Units (GPUs) have come to be increasingly used for general computation in scientific research. This field of GPU acceleration is now a vast and mature discipline. Molecular docking, the modeling of the interactions between two molecules, is a particularly computationally intensive task that has been the subject of research for many years. It is a critica
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De, Youngster Dela. "An Isometry-Invariant Spectral Approach for Macro-Molecular Docking." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/30226.

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Proteins and the formation of large protein complexes are essential parts of living organisms. Proteins are present in all aspects of life processes, performing a multitude of various functions ranging from being structural components of cells, to facilitating the passage of certain molecules between various regions of cells. The 'protein docking problem' refers to the computational method of predicting the appropriate matching pair of a protein (receptor) with respect to another protein (ligand), when attempting to bind to one another to form a stable complex. Research shows that matching th
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Tantar, Alexandru-Adrian. "Hybrid parallel metaheuristics for molecular docking on computational grids." Thesis, Lille 1, 2009. http://www.theses.fr/2009LIL10166.

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Cette thèse porte sur les méta-heuristiques hiérarchiques parallèles adaptatives pour l'échantillonnage conformationnel. Étant un problème hautement combinatoire et multlmodal, l'échantillonnage conformationnel requière la construction d'approches hybrides à large échelle. Après une analyse dei modèles mathématiques, nécessitant l'examen des différentes formulations du champ de force, nous avons proposé une étude des opérateurs de variation et des méthodes de recherche locale adaptés au problème ainsi que leur hybridation dynamique et adaptative. Cette étude nous a conduit à la proposition de
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BASCIU, ANDREA. "An enhanced-sampling MD-based protocol for molecular docking." Doctoral thesis, Università degli Studi di Cagliari, 2020. http://hdl.handle.net/11584/284135.

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Understanding molecular recognition of small molecules by proteins in atomistic detail is key for drug design. Molecular docking is a widely used computational method to mimic ligand-protein association in silico. However, predicting conformational changes occurring in proteins upon ligand binding is still a major challenge. Ensemble docking approaches address this issue by considering a set of different conformations of the protein obtained either experimentally or from computer simulations, e.g. from molecular dynamics. However, holo structures prone to host (the correct) ligands are
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DI, DOMIZIO ALESSANDRO. "Development of methodologies for molecular docking and their applications." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2009. http://hdl.handle.net/10281/7460.

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Virtual High Throughput Screening (vHTS) has an increasingly important role in lowering both costs and time in drug discovery. The present work deals with the development (C++ programming language) of a new molecular docking software (semi-flexible model) to be used for vHTS. It would improve some of the main aspects of this type of softwares in current use, with particular reference to the program AutoDock: a particular importance is given to the calculation of the ligand conformational energy variation in passing from the unbound to the bound state, which represents a crucial term in the doc
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Boyce, Sarah Emily. "Model systems for molecular docking: Understanding molecular recognition in polar and charged binding sites." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3390113.

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Salmaso, Veronica. "Exploring protein flexibility during docking to investigate ligand-target recognition." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3421817.

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Ligand-protein binding models have experienced an evolution during time: from the lock-key model to induced-fit and conformational selection, the role of protein flexibility has become more and more relevant. Understanding binding mechanism is of great importance in drug-discovery, because it could help to rationalize the activity of known binders and to optimize them. The application of computational techniques to drug-discovery has been reported since the 1980s, with the advent computer-aided drug design. During the years several techniques have been developed to address the protein flexibil
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Genheden, Samuel. "A fast protein-ligand docking method." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-69.

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<p>In this dissertation a novel approach to protein-ligand docking is presented. First an existing method to predict putative active sites is employed. These predictions are then used to cut down the search space of an algorithm that uses the fast Fourier transform to calculate the geometrical and electrostatic complementarity between a protein and a small organic ligand. A simplified hydrophobicity score is also calculated for each active site. The docking method could be applied either to dock ligands in a known active site or to rank several putative active sites according to their biologic
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Books on the topic "Molecular docking"

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Goldfeld, Dahlia A. Advances in structure and small molecule docking predictions for crystallized G-Protein coupled receptors. [publisher not identified], 2013.

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Vlachakis, Dimitrios P., ed. Molecular Docking. InTech, 2018. http://dx.doi.org/10.5772/intechopen.69830.

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Stefaniu, Amalia, ed. Molecular Docking and Molecular Dynamics. IntechOpen, 2019. http://dx.doi.org/10.5772/intechopen.77898.

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Stefaniu, Amalia. Molecular Docking and Molecular Dynamics. IntechOpen, 2019.

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Pospíšil, Pavel. Current problems in molecular docking. 2002.

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Molecular Docking - Recent Advances [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.100665.

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Molecular Docking for Computer-Aided Drug Design. Elsevier, 2021. http://dx.doi.org/10.1016/c2019-0-04960-6.

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De Brevern, Alexandre G., Ramanathan Sowdhamini, Agnel Praveen Joseph, and Joseph Rebehmed, eds. Advances in Molecular Docking and Structure-Based Modelling. Frontiers Media SA, 2022. http://dx.doi.org/10.3389/978-2-88974-509-8.

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B, Hari Prasath. Molecular Docking Studies of Plant Derived Compounds: Bioinformatics. LAP Lambert Academic Publishing, 2012.

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Wani, Tanveer A., Seema Zargar, and Afzal Hussain, eds. Spectroscopic, Thermodynamic and Molecular Docking Studies on Molecular Mechanisms of Drug Binding to Proteins. MDPI, 2023. http://dx.doi.org/10.3390/books978-3-0365-6225-4.

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Book chapters on the topic "Molecular docking"

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Morris, Garrett M., and Marguerita Lim-Wilby. "Molecular Docking." In Methods in Molecular Biology. Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-177-2_19.

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Banaganapalli, Babajan, Fatima A. Morad, Muhammadh Khan, et al. "Molecular Docking." In Essentials of Bioinformatics, Volume I. Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-02634-9_15.

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Bhandari, Amit, and Vibin Ramakrishnan. "Molecular Docking." In Springer Protocols Handbooks. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3405-9_2.

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Kumar, T. Durai Ananda. "Molecular Docking." In Drug Design: A Conceptual Overview. CRC Press, 2022. http://dx.doi.org/10.1201/9781003298755-8.

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Bortolato, Andrea, Marco Fanton, Jonathan S. Mason, and Stefano Moro. "Molecular Docking Methodologies." In Methods in Molecular Biology. Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-017-5_13.

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Cieślak, Dominika, Ivo Kabelka, and Damian Bartuzi. "Molecular Dynamics Simulations in Protein–Protein Docking." In Protein-Protein Docking. Springer US, 2024. http://dx.doi.org/10.1007/978-1-0716-3985-6_6.

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Bitencourt-Ferreira, Gabriela, and Walter Filgueira de Azevedo. "Docking with GemDock." In Methods in Molecular Biology. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9752-7_11.

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Bitencourt-Ferreira, Gabriela, and Walter Filgueira de Azevedo. "Docking with SwissDock." In Methods in Molecular Biology. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9752-7_12.

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Bitencourt-Ferreira, Gabriela, Val Oliveira Pintro, and Walter Filgueira de Azevedo. "Docking with AutoDock4." In Methods in Molecular Biology. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9752-7_9.

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Eyck, Lynn F. Ten, Jeffrey Mandell, Vladimir Kotlovyi, and Igor Tsigelny. "Fast Molecular Docking Methods." In Structure and Function of Cholinesterases and Related Proteins. Springer US, 1998. http://dx.doi.org/10.1007/978-1-4899-1540-5_98.

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Conference papers on the topic "Molecular docking"

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Lancellotti, Giacomo, Gianmarco Accordi, and Gianluca Palermo. "An Experimental Approach to Quantum Molecular Docking." In 2024 IEEE International Conference on Quantum Computing and Engineering (QCE). IEEE, 2024. https://doi.org/10.1109/qce60285.2024.00066.

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Atanu, Francis O., Estari Mamidala, Charles O. Nwonuma та Omookolade O. Alejolowo. "Molecular interactions between β-lactoglobulin protein and phytocannabinoids: a molecular docking and dynamics simulation study". У 2024 International Conference on Science, Engineering and Business for Driving Sustainable Development Goals (SEB4SDG). IEEE, 2024. http://dx.doi.org/10.1109/seb4sdg60871.2024.10630272.

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Ribeiro, Flávio Vinícius da Silva, Ricardo Morais de Miranda, and Solange Maria Vinagre Corrêa. "Aplicação do Docking Molecular para o melhoramento de fármacos." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol202052.

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Molecular docking uses theoretical chemistry and computer science resources to simulate, at the level of reality, chemical reactions involving molecules and macromolecules. Molecular docking was applied in the study of the interaction of an FX-CNT, evaluating the technique in the optimization of drugs.
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Ellingson, Sally R., and Jerome Baudry. "High-throughput virtual molecular docking." In the second international workshop. ACM Press, 2011. http://dx.doi.org/10.1145/1996023.1996028.

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Samarskaya, Viktoriya, Aleksandr Kovalenko, Galina Sroslova, Margarita Postnova, Aleksandr Shiroky, and Andrei Serov. "Molecular docking data preparation tool." In Saratov Fall Meeting 2018: Computations and Data Analysis: from Nanoscale Tools to Brain Functions, edited by Dmitry E. Postnov. SPIE, 2019. http://dx.doi.org/10.1117/12.2522533.

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Xiao, Yong L., and Donald E. Williams. "Molecular docking using genetic algorithms." In the 1994 ACM symposium. ACM Press, 1994. http://dx.doi.org/10.1145/326619.326721.

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Brindha, M., R. Shelishiyah, and S. Vasanthavalli. "Molecular Docking Analysis Of CFTR Inhibitors." In 2020 Sixth International Conference on Bio Signals, Images, and Instrumentation (ICBSII). IEEE, 2020. http://dx.doi.org/10.1109/icbsii49132.2020.9167624.

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Solis-Vasquez, Leonardo, Diogo Santos-Martins, Andreas F. Tillack, Andreas Koch, Jerome Eberhardt, and Stefano Forli. "Parallelizing Irregular Computations for Molecular Docking." In 2020 IEEE/ACM 10th Workshop on Irregular Applications: Architectures and Algorithms (IA3). IEEE, 2020. http://dx.doi.org/10.1109/ia351965.2020.00008.

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Roh, Youngtae, Jun Lee, Sungjun Park, and Jee-In Kim. "A molecular docking system using CUDA." In the 2009 International Conference. ACM Press, 2009. http://dx.doi.org/10.1145/1644993.1644999.

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Silva Moraes, Rafael, and Fernando Gomes de Souza Junior. "Mineração de dados sobre molecular docking." In 2a Conferência Brasileira de Planejamento Experimental e Análise de Dados. Even3, 2022. http://dx.doi.org/10.29327/conbrapa2022.558289.

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Reports on the topic "Molecular docking"

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Kotwal, Shashikant. Grant: Automation of BitterX Molecular Docking of Bitter taste compounds to Human Bitter Taste Receptors (TAS2R). ResearchHub Technologies, Inc., 2025. https://doi.org/10.55277/researchhub.b0nzqfac.

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Benial. A, Milton Franklin, Pandi Meena. G, Mathavan Thangapandian, and James Jebaseelan Samuel. E. Quantum chemical, spectroscopic and molecular docking investigations of potential pulmonary fibrosis drug methyl 2-chloro 4-iodonicotinate. Peeref, 2023. http://dx.doi.org/10.54985/peeref.2306p9633440.

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Rafaeli, Ada, Russell Jurenka, and Chris Sander. Molecular characterisation of PBAN-receptors: a basis for the development and screening of antagonists against Pheromone biosynthesis in moth pest species. United States Department of Agriculture, 2008. http://dx.doi.org/10.32747/2008.7695862.bard.

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The original objectives of the approved proposal included: (a) The determination of species- and tissue-specificity of the PBAN-R; (b) the elucidation of the role of juvenile hormone in gene regulation of the PBAN-R; (c) the identificationof the ligand binding domains in the PBAN-R and (d) the development of efficient screening assays in order to screen potential antagonists that will block the PBAN-R. Background to the topic: Moths constitute one of the major groups of pest insects in agriculture and their reproductive behavior is dependent on chemical communication. Sex-pheromone blends are
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Judson, R. S., E. P. Jaeger, and A. M. Treasurywala. A genetic algorithm based method for docking flexible molecules. Office of Scientific and Technical Information (OSTI), 1993. http://dx.doi.org/10.2172/10132318.

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Jha, Ramesh, Sang-Min Shin, and Taraka Dale. Rosetta Comparative Modeling and Ligand Docking for a Transcription Factor Library Design to Select Biosensor for an Anthropogenic Molecule. Office of Scientific and Technical Information (OSTI), 2022. http://dx.doi.org/10.2172/1871442.

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Gurevitz, Michael, William A. Catterall, and Dalia Gordon. face of interaction of anti-insect selective toxins with receptor site-3 on voltage-gated sodium channels as a platform for design of novel selective insecticides. United States Department of Agriculture, 2013. http://dx.doi.org/10.32747/2013.7699857.bard.

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Voltage-gated sodium channels (Navs) play a pivotal role in excitability and are a prime target of insecticides like pyrethroids. Yet, these insecticides are non-specific due to conservation of Navs in animals, raising risks to the environment and humans. Moreover, insecticide overuse leads to resistance buildup among insect pests, which increases misuse and risks. This sad reality demands novel, more selective, insect killers whose alternative use would avoid or reduce this pressure. As highly selective insect toxins exist in venomous animals, why not exploit this gift of nature and harness t
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