Results 331 to 340 of about 452,634 (352)

Integrating Molecular Docking and Molecular Dynamics Simulations

2019
Computational methods, applied at the early stages of the drug design process, use current technology to provide valuable insights into the understanding of chemical systems in a virtual manner, complementing experimental analysis. Molecular docking is an in silico method employed to foresee binding modes of small compounds or macromolecules in contact
Rafaela Salgado Ferreira, Ernesto Raul Caffarena, Lucianna Helene Santos   +2 more
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Protein docking algorithms: simulating molecular recognition

Current Opinion in Structural Biology, 1993
Docking 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 ...
Joël Janin, Jacqueline Cherfils
openaire   +2 more sources

Bio-Inspired Algorithms Applied to Molecular Docking Simulations

Current Medicinal Chemistry, 2011
Nature 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).
W. F. de Azevedo, G. Heberle
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The Interaction of Isoflavone Phytoestrogens with ERα and ERβ by Molecular Docking and Molecular Dynamics Simulations

Current Computer-Aided Drug Design, 2021
Aim and Objective: Isoflavone phytoestrogens, commonly present in natural plants, are closely related to human health. The combination of them with estrogen receptors in the body can play an important role in the prevention and treatment of cardiovascular diseases, cancer, and menopausal diseases. This research is conducted for the wider application
Feng Luan, Ting Wang, Chunyan Zhao, Yaquan Liu, Xuming Zhuang   +4 more
openaire   +3 more sources

Distance-constrained molecular docking by simulated annealing

"Protein Engineering, Design and Selection", 1990
An 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 docking, 3D-QASR and molecular dynamics simulations of thiazoles Pin1 inhibitors

Journal of Biomolecular Structure and Dynamics, 2021
Pin1 (protein interacting with never-in-mitosis akinase-1) is a member of the PPIase (peptidylprolyl cis-trans isomerase) family. It can interact with a variety of carcinogenic or tumor suppressive phosphorylated proteins. The interaction results in the conformational changes of target proteins, and ultimately regulates the activity of these proteins ...
Lina Ding, Jiangheng Zhao, Ruiyou Chen, Jieying Zang, Min Liu, Xin Zhao, Shuangshuang Yang   +6 more
openaire   +3 more sources

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
openaire   +3 more sources

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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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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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
openaire   +3 more sources