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MCDOCK: A Monte Carlo simulation approach to the molecular docking problem
Journal of Computer-Aided Molecular Design, 1999Prediction of the binding mode of a ligand (a drug molecule) to its macromolecular receptor, or molecular docking, is an important problem in rational drug design. We have developed a new docking method in which a non-conventional Monte Carlo (MC) simulation technique is employed.
Ming Liu, Shaomeng Wang
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Distance-constrained molecular docking by simulated annealing
"Protein Engineering, Design and Selection", 1990An optimized method based on the principle of simulated annealing is presented for determining the relative position and orientation of interacting molecules. The spatial relationships of these molecules are described by intermolecular distance constraints between specific pairs of atoms, such as found in hydrogen bonds or from experimentally ...
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Protein docking algorithms: simulating molecular recognition
Current Opinion in Structural Biology, 1993Docking algorithms simulate protein-protein association in molecular assemblies such as protease-inhibitor or antigen-antibody complexes by reconstituting the complexes from their component molecules. They not only efficiently retrieve native structures but also select a number of non-native structures with structural and physicochemical features that ...
Jacqueline Cherfils, Joël Janin
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Simulation of Carbohydrates, from Molecular Docking to Dynamics in Water
2012Modeling of carbohydrates is particularly challenging because of the variety of structures resulting for the high number of monosaccharides and possible linkages and also because of their intrinsic flexibility. The development of carbohydrate parameters for molecular modeling is still an active field.
Nicolas, Sapay +2 more
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Effect of preprocessing and simulation parameters on the performance of molecular docking studies
Journal of Molecular Modeling, 2023Molecular docking is an important and rapid tool that provides a comprehensive view of different molecular mechanisms. It is often used to verify the binding interactions of many pairs of molecules and is much faster than more rigorous approaches.
Pedro Henrique, Callil-Soares +2 more
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Journal of Molecular Graphics and Modelling, 2017
Ammoniated lignin, prepared through the Mannich reaction of lignin, has more advantages as a slow-release carrier of urea molecules than ammoxidized lignin and lignin. The advantages of the ammoniated lignin include its amine groups added and its high molecular mass kept as similar as that of lignin.
Wenzhuo, Li +4 more
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Ammoniated lignin, prepared through the Mannich reaction of lignin, has more advantages as a slow-release carrier of urea molecules than ammoxidized lignin and lignin. The advantages of the ammoniated lignin include its amine groups added and its high molecular mass kept as similar as that of lignin.
Wenzhuo, Li +4 more
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Molecular docking and molecular dynamics simulation studies of GPR40 receptor–agonist interactions
Journal of Molecular Graphics and Modelling, 2010In order to explore the agonistic activity of small-molecule agonists to GPR40, AutoDock and GROMACS software were used for docking and molecular dynamics studies. A molecular docking of eight structurally diverse agonists (six carboxylic acids (CAs) agonist, and two non-carboxylic acids (non-CAs) agonist) was performed and the differences in their ...
Shao-Yong, Lu +5 more
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Molecular Pharmaceutics, 2013
While the effects of hydrophilic excipients in enhancing the dissolution rate of water-insoluble drugs have been validated, the underlying mechanism remains poorly understood, particularly at a molecular level. In this work, a combination of docking calculations and MD simulations was applied to investigate the molecular interactions between ...
Caixia, Li +3 more
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While the effects of hydrophilic excipients in enhancing the dissolution rate of water-insoluble drugs have been validated, the underlying mechanism remains poorly understood, particularly at a molecular level. In this work, a combination of docking calculations and MD simulations was applied to investigate the molecular interactions between ...
Caixia, Li +3 more
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Molecular Docking and Molecular Dynamics Simulation of New Potential JAK3 Inhibitors
Current Computer-Aided Drug DesignIntroduction: JAK3 kinase inhibitor has become an effective means to treat tumors and autoimmune diseases. Methods: In this study, molecular docking and molecular dynamics simulation were used to study the theoretical interaction mechanism between 1-phenylimidazolidine-2-one molecules and JAK3 protein Results: The results of molecular docking ...
Qidi, Zhong +4 more
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Molecular Dynamics Simulations in Protein–Protein Docking
Concerted interactions between all the cell components form the basis of biological processes. Protein-protein interactions (PPIs) constitute a tremendous part of this interaction network. Deeper insight into PPIs can help us better understand numerous diseases and lead to the development of new diagnostic and therapeutic strategies.Dominika, Cieślak +2 more
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