Results 261 to 270 of about 107,002 (300)

Molecular docking and molecular dynamics simulation studies of GPR40 receptor–agonist interactions

Journal of Molecular Graphics and Modelling, 2010
In 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, Yong-Jun, Jiang, Jing, Lv, Tian-Xing, Wu, Qing-Sen, Yu, Wei-Liang, Zhu   +5 more
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Synthesis, anticholinesterase activity, molecular docking, and molecular dynamic simulation studies of 1,3,4‐oxadiazole derivatives

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, Asaf E. Evren, Begüm N. Sağlık, Leyla Yurttaş, Naime F. Tay   +4 more
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ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation

The Journal of Physical Chemistry B, 2018
We 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, Chika Sato, Akio Kitao   +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, Ivo, Kabelka, Damian, Bartuzi   +2 more
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Molecular Docking and Molecular Dynamics Simulation of New Potential JAK3 Inhibitors

Current Computer-Aided Drug Design
Introduction: 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, Jiarui, Qin, Kaihui, Zhao, Lihong, Guo, Dongmei, Li   +4 more
openaire   +2 more sources

Molecular modeling, simulation and docking study of ebola virus glycoprotein

Journal of Molecular Graphics and Modelling, 2017
Ebola 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, Aqsa, Farman, Syed Lal, Badshah, Ata, Ur Rahman, Haroon, Ur Rashid, Khalid, Khan   +5 more
openaire   +2 more sources

Fully Flexible Docking via Reaction-Coordinate-Independent Molecular Dynamics Simulations

Journal of Chemical Information and Modeling, 2018
Predicting the geometry of protein-ligand binding complexes is of primary importance for structure-based drug discovery. Molecular dynamics (MD) is emerging as a reliable computational tool for use in conjunction with, or an alternative to, docking methods. However, simulating the protein-ligand binding process often requires very expensive simulations.
BERTAZZO, MARTINA, BERNETTI, MATTIA, Recanatini, Maurizio, Masetti, Matteo, Cavalli, Andrea   +4 more
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Molecular docking and molecular dynamics simulation studies on PLCE1 encoded protein

Journal of Molecular Structure, 2019
Abstract Phospholipase C epsilon gene (PLCE1) is encoded the 1-phosphatidylinositol 4,5- bisphosphate phosphodiesterase ɛ-1 protein. This protein is characterized by the fetal onset of enormous proteinuria following by severe steroid resistance nephrotic syndrome (SRNS). The mutation position is located on the PIPLC_X domain of PLCE1 encoded protein.
Satya Narayan Sahu, Subrat Kumar Pattanayak   +1 more
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Molecular docking, 3D-QASR and molecular dynamics simulations of benzimidazole Pin1 inhibitors

Physical Chemistry Chemical Physics
Molecular docking, 3D-QSAR, dynamics simulations, free energy and decomposition calculation between Pin1 protein and benzimidazole Pin1 inhibitors.
Min Liu, Bingli Wang, Huan Liu, Haolun Xia, Lina Ding   +4 more
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Molecular docking and molecular dynamics simulation decoding molecular mechanism of EDCs binding to hERRγ

Journal of Molecular Modeling
Human estrogen-related receptor γ (hERRγ) is a key protein involved in various endocrines and metabolic signaling. Numerous environmental endocrine-disrupting chemicals (EDCs) can impact related physiological activities through receptor signaling pathways.
Ying, Sun, Lin, Chen, Bing, Zhao, Ruige, Wang   +3 more
openaire   +2 more sources