Structural insights into the binding mode of d-sorbitol with sorbitol dehydrogenase using QM-polarized ligand docking and molecular dynamics simulations

2016 ◽  
Vol 114 ◽  
pp. 244-256 ◽  
Author(s):  
Chandrabose Selvaraj ◽  
Gopinath Krishnasamy ◽  
Sujit Sadashiv Jagtap ◽  
Sanjay K.S. Patel ◽  
Saurabh Sudha Dhiman ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Mode ◽  
Sorbitol Dehydrogenase ◽  
Ligand Docking ◽  
Dynamics Simulations ◽  
Structural Insights

Pyrrolidine Derivatives as Plasmepsin Inhibitors: Binding Mode Analysis Assisted by Molecular Dynamics Simulations of a Highly Flexible Protein

ChemMedChem ◽  
2010 ◽  
Vol 5 (3) ◽  
pp. 443-454 ◽  
Author(s):  
Torsten Luksch ◽  
Andreas Blum ◽  
Nina Klee ◽  
Wibke E. Diederich ◽  
Christoph A. Sotriffer ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Mode ◽  
Mode Analysis ◽  
Flexible Protein ◽  
Dynamics Simulations

Revealing the binding mode between respiratory syncytial virus fusion protein and benzimidazole-based inhibitors

2015 ◽  
Vol 11 (7) ◽  
pp. 1857-1866
Author(s):  
Dingjue Ji ◽  
Wei Ye ◽  
HaiFeng Chen
Keyword(s):  
Molecular Dynamics ◽  
Respiratory Syncytial Virus ◽  
Fusion Protein ◽  
Molecular Dynamics Simulations ◽  
Binding Mode ◽  
Virus Fusion ◽  
Syncytial Virus ◽  
Dynamics Simulations

The binding mode between benzimidazole-based inhibitors and RSVF protein was revealed by docking and molecular dynamics simulations.

scholarly journals Molecular Dynamics Simulations for Biological Systems

2017 ◽  
pp. 1044-1071 ◽  
Author(s):  
Prerna Priya ◽  
Minu Kesheri ◽  
Rajeshwar P. Sinha ◽  
Swarna Kanchan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Biological Molecules ◽  
Dynamics Simulation ◽  
Ligand Docking ◽  
Protein Protein Interaction ◽  
Dynamics Simulations

Molecular dynamics simulation is an important tool to capture the dynamicity of biological molecule and the atomistic insights. These insights are helpful to explore biological functions. Molecular dynamics simulation from femto seconds to milli seconds scale give a large ensemble of conformations that can reveal many biological mysteries. The main focus of the chapter is to throw light on theories, requirement of molecular dynamics for biological studies and application of molecular dynamics simulations. Molecular dynamics simulations are widely used to study protein-protein interaction, protein-ligand docking, effects of mutation on interactions, protein folding and flexibility of the biological molecules. This chapter also deals with various methods/algorithms of protein tertiary structure prediction, their strengths and weaknesses.

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