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Simulating molecular docking with haptics. [PDF]

, 2015
Intermolecular binding underlies various metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow the study of the binding process.
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Studies of Bicalutamide–Excipients Interaction by Combination of Molecular Docking and Molecular Dynamics Simulation

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, Jie-Xin, Wang, Yuan, Le, Jian-Feng, Chen   +3 more
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Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6

Journal of Chemical Information and Modeling, 2009
Active-site water molecules form an important component in biological systems, facilitating promiscuous binding or an increase in specificity and affinity. Taking water molecules into account in computational approaches to drug design or site-of-metabolism predictions is currently far from straightforward.
Rita Santos, Jozef Hritz, Chris Oostenbrink   +2 more
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Molecular Dynamics Simulation and Docking of MUC1 O-Glycopeptide

Advances in computer performance and computational simulations allow increasing sophistication in applications in biological systems. Molecular dynamics (MD) simulations are especially suitable for studying conformation, dynamics, and interaction of flexible biomolecules such as free glycans and glycopeptides.
Ryoka, Kokubu, Shiho, Ohno, Noriyoshi, Manabe, Yoshiki, Yamaguchi   +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
Nasir, Ahmad, Aqsa, Farman, Syed Lal, Badshah, Ata, Ur Rahman, Haroon, Ur Rashid, Khalid, Khan   +5 more
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Molecular Docking and Simulation in Drug Discovery: A Review

International Journal of Research and Innovation in Applied Science
Drug discovery is a complex, time-consuming, and costly process that requires the identification and optimization of potential therapeutic compounds. In recent years, computational approaches such as molecular docking and molecular dynamics (MD) simulation have significantly transformed modern drug design.
Iffat Hussain, Amit KumarAhirwar, Divya Patel, Aftab Khan, Farman Hussain, Rishabh Tiwari, Atul kumar   +6 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
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Refactoring the Molecular Docking Simulation for Heterogeneous, Manycore Processors Systems

2017 IEEE International Symposium on Parallel and Distributed Processing with Applications and 2017 IEEE International Conference on Ubiquitous Computing and Communications (ISPA/IUCC), 2017
This paper presents a scalable design and implementation of the molecular docking application DOCK for a large-scale high performance computing system, the Sunway TaihuLight supercomputer, which provisions a heterogeneous, manycore processor architecture that consists of management processing elements (MPEs) and clusters of computing processing ...
Junshi Chen 0003, Han Lin, Weihao Liang, Yang Yu, Wenting Han, Hong An, Yong Chen 0001, Xin Liu 0081   +7 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.
Fábio Alberto, de Molfetta, Renato Ferreira, de Freitas, Albérico Borges Ferreira, da Silva, Carlos Alberto, Montanari   +3 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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