Journal ArticleDOI
Identification of novel and selective agonists for ABA receptor PYL3.
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TLDR
The structural basis of the binding mechanism of 3-methyleneisoindolin-1-one molecules with ABA receptors is revealed and Mol26 and Mol25 were identified for the development of specific PYL3 agonists with a vast potential in agriculture to accentuate the ABA like action in plants.About:
This article is published in Plant Physiology and Biochemistry.The article was published on 2020-09-01. It has received 16 citations till now. The article focuses on the topics: Pyrabactin & Abscisic acid.read more
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Abiotic stress responses in plants.
TL;DR: In this paper, the molecular mechanisms underlying the responses of plants to abiotic stresses emphasizes their multilevel nature; multiple processes are involved, including sensing, signalling, transcription, transcript processing, translation and post-translational protein modifications.
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Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs.
TL;DR: The D SPD-2, DSPD-6, and DSPd-5 could be developed as potential inhibitors of SARS-CoV-2 by targeting molecules to bind effectively to the S1 subsite of the Mpro binding pocket.
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Himalayan bioactive molecules as potential entry inhibitors for the human immunodeficiency virus.
TL;DR: In this paper, bioactive molecules from different Himalayan plants were screened considering their potential to bind with the CCR5 and CXCR4 co-receptors and found that Butyl 2-ethylhexyl phthalate and Dactylorhin-A showed a higher binding affinity with CCR 5 coreceptor than the standard antagonist Maraviroc.
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Benchmarking the ability of novel compounds to inhibit SARS-CoV-2 main protease using steered molecular dynamics simulations
Rahul Singh,Vijayant Bhardwaj,Pralay Das,Dhananjay Bhattacherjee,Grigory V. Zyryanov,Rituraj Purohit +5 more
TL;DR: In this article , the potential binding mechanisms of 1,2,3-triazole scaffolds in comparison to co-crystallized inhibitors 11a and 11b towards SARS-CoV-2 main protease (Mpro) were explored.
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In silico drug repositioning based on the integration of chemical, genomic and pharmacological spaces.
TL;DR: Wang et al. as mentioned in this paper collected three different types of drug features (i.e., chemical, genomic and pharmacological spaces) from public databases and further developed a fusion method to combine the three similarity measurements.
References
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Molecular dynamics with coupling to an external bath.
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
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A smooth particle mesh Ewald method
TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
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GROMACS: Fast, flexible, and free
David van der Spoel,Erik Lindahl,Berk Hess,Gerrit Groenhof,Alan E. Mark,Herman J. C. Berendsen +5 more
TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
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PRODRG: a tool for high-throughput crystallography of protein–ligand complexes
TL;DR: The small-molecule topology generator PRODRG is described, which takes input from existing coordinates or various two-dimensional formats and automatically generates coordinates and molecular topologies suitable for X-ray refinement of protein-ligand complexes.
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Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
Peter A. Kollman,Irina Massova,Carolina M. Reyes,Bernd Kuhn,Shuanghong Huo,Lillian T. Chong,Matthew Lee,Tai-Sung Lee,Yong Duan,Wei Wang,Oreola Donini,Piotr Cieplak,Jaysharee Srinivasan,David A. Case,Thomas E. Cheatham +14 more
TL;DR: A historical perspective on the application of molecular dynamics to biological macromolecules is presented and recent developments combining state-of-the-art force fields with continuum solvation calculations have allowed for the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free energies from molecular dynamics trajectories.