Journal ArticleDOI
Molecular mechanics and quantum chemical calculations unveil the combating effect of baicalein on human islet amyloid polypeptide aggregates
TLDR
This study studies the disaggregation mechanism of naturally occurring polyphenol baicalein, obtained from the roots of S. baicalensis and Indian trumpet flower on hIAPP dimer using quantum chemical calculation and discrete molecular dynamics to bridging the gap for future therapeutic strategy in designing the anti-aggregation compounds that inhibit hI APP amyloids.Abstract:
Formation of insoluble toxic aggregates by hIAPP polypeptide is found to be a core component for disease pathogenicity of patients suffering from type II diabetes. Naturally occurring polyp...read more
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Discrete molecular dynamics studies of the folding of a protein-like model
TL;DR: In this article, a discrete time molecular dynamics algorithm was proposed to resolve the folding of a protein model. But the algorithm is computationally heavy and it is not suitable for high computational complexity.
Journal ArticleDOI
Alpha-Synuclein Aggregation in Parkinson's Disease.
E. Srinivasan,E. Srinivasan,G. Chandrasekhar,P. Chandrasekar,K. Anbarasu,A.S. Vickram,Rohini Karunakaran,R. Rajasekaran,P. S. Srikumar +8 more
TL;DR: Parkinson's disease (PD) is characterized by distinct aging-independent loss of dopaminergic neurons in substantia nigra pars compacta (SNpc) region urging toward neuronal loss as discussed by the authors.
Journal ArticleDOI
Probing the competitive inhibitor efficacy of frog-skin alpha helical AMPs identified against ACE2 binding to SARS-CoV-2 S1 spike protein as therapeutic scaffold to prevent COVID-19
Ponnusamy Chandra Sekar,E. Srinivasan,G. Chandrasekhar,D. Meshach Paul,G. Sanjay,Sankuratri Surya,NS. Arun Raj Kumar,R. Rajasekaran +7 more
TL;DR: In this article , a comparative study of intermolecular interactions between SARS-CoV-2 spike protein S1 and AMPs was performed relative to S1-ACE2p interactions.
Journal ArticleDOI
A review on Huntington protein Insight into protein aggregation and therapeutic interventions.
TL;DR: The mechanism proposed towards the formation of HTT protein aggregation and the impact of therapeutic strategies for the treatment of HD are reviewed.
Journal ArticleDOI
Illustrating the Effect of Small Molecules Derived from Natural Resources on Amyloid Peptides.
Rituparna Sinha Roy,Sandip Paul +1 more
TL;DR: In this paper , the authors summarize some of the most important natural small molecular probes which can inhibit the aggregation of Aβ, hIAPP, and α-syn peptides and discuss how their binding efficacy and preference for the peptides vary with their structure and conformation.
References
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Journal ArticleDOI
Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
TL;DR: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms.
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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Garrett M. Morris,Ruth Huey,William Lindstrom,Michel F. Sanner,Richard K. Belew,David S. Goodsell,Arthur J. Olson +6 more
TL;DR: AutoDock4 incorporates limited flexibility in the receptor and its utility in analysis of covalently bound ligands is reported, using both a grid‐based docking method and a modification of the flexible sidechain technique.
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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
TL;DR: A new implementation of the molecular simulation toolkit GROMACS is presented which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines.
Journal ArticleDOI
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
Garrett M. Morris,David S. Goodsell,Robert Scott Halliday,Ruth Huey,William E. Hart,Richard K. Belew,Arthur J. Olson +6 more
TL;DR: It is shown that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTODOCK, and that the Lamarckia genetic algorithm is the most efficient, reliable, and successful of the three.
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Molecular dynamics simulations at constant pressure and/or temperature
TL;DR: In this paper, it is shown that time averages of properties of the simulated fluid are equal to averages over the isoenthalpic-isobaric, canonical, and isothermal-isboric ensembles.