Results 331 to 340 of about 449,170 (361)

MCDOCK: A Monte Carlo simulation approach to the molecular docking problem

Journal of Computer-Aided Molecular Design, 1999
Prediction 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.
Shaomeng Wang, Ming Liu
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Simulation of Carbohydrates, from Molecular Docking to Dynamics in Water

2012
Modeling 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.
Alessandra Nurisso, Nicolas Sapay, Anne Imberty   +2 more
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Docking and molecular dynamics simulation of quinone compounds with trypanocidal activity

Journal of Molecular Modeling, 2009
In this work, two different docking programs were used, AutoDock and FlexX, which use different types of scoring functions and searching methods. The docking poses of all quinone compounds studied stayed in the same region in the trypanothione reductase. This region is a hydrophobic pocket near to Phe396, Pro398 and Leu399 amino acid residues.
Carlos A. Montanari, Albérico B. F. da Silva, Renato F. Freitas, Fábio Alberto de Molfetta   +3 more
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Effect of preprocessing and simulation parameters on the performance of molecular docking studies

Journal of Molecular Modeling, 2023
Molecular 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, Lilian Caroline Kramer, Biasi, Pedro de Alcântara, Pessoa Filho   +2 more
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BACE1 Inhibition by Genistein: Biological Evaluation, Kinetic Analysis, and Molecular Docking Simulation.

Journal of Medicinal Food, 2018
β-site amyloid precursor protein cleaving enzyme 1 (BACE1) plays a role in generating amyloid β (Aβ), thus playing a major part early in the pathogenesis of Alzheimer's disease (AD). BACE1 has emerged as a crucial therapeutic target for decreasing the Aβ
Kumju Youn, Jihyun Park, Seonah Lee, Seung-Eun Lee, Jinhyuk Lee, E. Yun, W. Jeong, Mira Jun   +7 more
semanticscholar   +1 more source

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
Haroon Ur Rashid, Syed Lal Badshah, Nasir Ahmad, Aqsa Farman, Ata Ur Rahman, Khalid Khan   +5 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 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 analyses of urea with ammoniated and ammoxidized lignin

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.
Jiangshan Zhao, Song Zhang, Huang Shuaiyu, Li Wenzhuo, Yingying Zhao   +4 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
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