Adaptive BP-Dock: An Induced Fit Docking Approach for Full Receptor Flexibility

2016 ◽  
Vol 56 (4) ◽  
pp. 734-746 ◽  
Author(s):  
Ashini Bolia ◽  
S. Banu Ozkan
Keyword(s):  
Induced Fit Docking ◽  
Induced Fit ◽  
Receptor Flexibility ◽  
Docking Approach

Induced-Fit Docking Approach Provides Insight into the Binding Mode and Mechanism of Action of HIV-1 Integrase Inhibitors

ChemMedChem ◽  
2009 ◽  
Vol 4 (9) ◽  
pp. 1446-1456 ◽  
Author(s):  
Maria Letizia Barreca ◽  
Nunzio Iraci ◽  
Laura De Luca ◽  
Alba Chimirri
Keyword(s):  
Mechanism Of Action ◽  
Binding Mode ◽  
Integrase Inhibitors ◽  
Induced Fit Docking ◽  
Induced Fit ◽  
Docking Approach ◽  
Insight Into ◽  
Hiv 1

scholarly journals Identification of Gly/NMDAR Antagonist from Chromolaena odorata’s Derived Phytoconstituents using Induced Fit Docking Approach

2019 ◽  
Author(s):  
Temitope Israel David ◽  
Olaposi Idowu. Omotuyi ◽  
Olalekan David Agboola ◽  
Dominic Chinedu Okonkwo ◽  
Niyi Samuel Adelakun
Keyword(s):  
Nmda Receptor ◽  
Ferulic Acid ◽  
Caffeic Acid ◽  
Binding Affinity ◽  
Receptor Site ◽  
Antagonistic Effect ◽  
Induced Fit Docking ◽  
Induced Fit ◽  
Docking Score ◽  
Docking Approach

AbstractThe ionotropic activation of N-methyl-D-aspartic acid (NMDA) plays a significant role in different type of neurodegenerative disease, as it is a tetramer with two Glycine binding subunit and two glutamate subunits. NMDA receptor can be inhibited by either blocking of the glycine site or glutamate site. Previously reported inhibitors of NMDA receptor focus on the inhibition of the glutamate subunit, which was reported to be associated with side effects such as ataxia, memory deficits, neurotoxicity. Therefore, different compounds with antagonistic effect are been explored on Gly/NMDA site. Glide XP docking was employed in screening phyto-constituent of Chromolaena odorata against Gly/NMDA receptor for hit compounds with antagonistic properties. The hit compounds were further subjected to Induced fit docking (IFD) and lipinski rule of five. The final selection was based on Rigid XP docking score using co-crystallized ligand as threshold docking score, interaction with receptor site residues, and IFD score. Ferulic acid, caffeic acid and scutellarein recorded binding affinity of −8.752Kcal/mol, 10.004 Kcal/mol and - 9.096 Kcal/mol respectively, which is higher than the binding affinity of co-crystallized ligand. Induced fit score obtained were −614.38, −614.03 and −616.31 for ferulic acid, caffeic acid and scutellarein respectively. The Adme properties of the phyto-constituent indicated that the compounds are drug-like in nature.

Designing of CHK1 Inhibitors by 3d-QSAR, Virtual Screening and Induced Fit Docking Studies

2015 ◽  
Vol 109 (12) ◽  
pp. 2271 ◽  
Author(s):  
Sayalee Chavan ◽  
Rajkumar Hirwani ◽  
M. Sarwar Alam ◽  
Nikhil Vidyasagar ◽  
Radhacharan Dash ◽  
...  
Keyword(s):  
Virtual Screening ◽  
3D Qsar ◽  
Docking Studies ◽  
Induced Fit Docking ◽  
Induced Fit

scholarly journals Induced fit docking, and the use of QM/MM methods in docking

2013 ◽  
Vol 10 (3) ◽  
pp. e411-e418 ◽  
Author(s):  
Mengang Xu ◽  
Markus A. Lill
Keyword(s):  
Induced Fit Docking ◽  
Induced Fit

scholarly journals Fleksy: a flexible approach to induced fit docking

2010 ◽  
Vol 2 (S1) ◽  
Author(s):  
Markus Wagener ◽  
SB Nabuurs ◽  
J de Vlieg
Keyword(s):  
Induced Fit Docking ◽  
Induced Fit ◽  
Flexible Approach
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