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Web Services for Molecular Docking Simulations
2019Docking process is one of the most significant activities for the analysis of protein-protein or protein-ligand complexes. These tools have become of unique importance when allocated in web services, collaborating scientifically with several areas of knowledge in an interdisciplinary way.
Nelson J F, da Silveira +3 more
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Bio-Inspired Algorithms Applied to Molecular Docking Simulations
Current Medicinal Chemistry, 2011Nature as a source of inspiration has been shown to have a great beneficial impact on the development of new computational methodologies. In this scenario, analyses of the interactions between a protein target and a ligand can be simulated by biologically inspired algorithms (BIAs).
G, Heberlé, W F, de Azevedo
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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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Molecular dynamics simulation of the docking of substrates to proteins
Proteins: Structure, Function, and Bioinformatics, 1994AbstractA simple method is described to perform docking of subtrates to proteins or probes to receptor molecules by a modification of molecular dynamics simulations. The method consists of a separation of the center‐of‐mass motion of the substrate from its internal and rotational motions, and a separate coupling to different thermal baths for both ...
DINOLA, A, ROCCATANO, D, BERENDSEN, HJC
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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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Archiv der Pharmazie, 2022
AbstractTwo new series of 1,3,4‐oxadiazoles bearing pyridine and thiazole heterocycles (4a‐h and 5a‐h) were synthesized (2,5‐disubstituted‐1,3,4‐oxadiazoles). The structures of these newly synthesized compounds were confirmed by 1H nuclear magnetic resonance (NMR), 13C NMR, high‐resolution mass spectrometric and Fourier transform infrared spectroscopic
Şeyma Durmaz +4 more
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AbstractTwo new series of 1,3,4‐oxadiazoles bearing pyridine and thiazole heterocycles (4a‐h and 5a‐h) were synthesized (2,5‐disubstituted‐1,3,4‐oxadiazoles). The structures of these newly synthesized compounds were confirmed by 1H nuclear magnetic resonance (NMR), 13C NMR, high‐resolution mass spectrometric and Fourier transform infrared spectroscopic
Şeyma Durmaz +4 more
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ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation
The Journal of Physical Chemistry B, 2018We propose a simple but efficient and accurate method to generate protein-ligand complex structures, called Concentrated ligand Docking (ColDock). This method consists of multiple independent molecular dynamics simulations in which ligands are initially distributed randomly around a protein at relatively high concentration (∼100 mM).
Kazuhiro Takemura +2 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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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 modeling, simulation and docking study of ebola virus glycoprotein
Journal of Molecular Graphics and Modelling, 2017Ebola virus (EBOV) is a filamentous, enveloped, non-segmented, negative-strand ribonucleic acid (RNA) virus which belongs to family Filoviridae. Ebola virus includes different glycoproteins each of which plays their roles in different aspects of viral life cycle. In this study secreted glycoprotein (Q7T9E0) of Ebola virus was acquired from Uniprot. The
Nasir, Ahmad +5 more
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