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Scalable Molecular Dynamics with NAMD
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The article was published on 2012-12-14 and is currently open access. It has received 13375 citations till now.read more
Citations
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Factors influencing local membrane curvature induction by N-BAR domains as revealed by molecular dynamics simulations.
TL;DR: It is found that the strong curvature induction observed in the previous simulations requires the stable presentation of the charged concave surface to the membrane and is not driven by the membrane-embedded amphipathic helices.
Journal ArticleDOI
Atazanavir, Alone or in Combination with Ritonavir, Inhibits SARS-CoV-2 Replication and Proinflammatory Cytokine Production.
Natalia Fintelman-Rodrigues,Carolina Q. Sacramento,Carlyle Ribeiro Lima,Franklin Souza da Silva,André C. Ferreira,Mayara Mattos,Caroline S. de Freitas,Vinicius Cardoso Soares,Suelen da Silva Gomes Dias,Jairo R. Temerozo,Milene D. Miranda,Aline R. Matos,Fernando A. Bozza,Nicolas Carels,Carlos Roberto Alves,Marilda M. Siqueira,Patrícia T. Bozza,Thiago Moreno L. Souza +17 more
TL;DR: ATV inhibits SARS-CoV-2 replication, alone or in combination with ritonavir (RTV) in Vero cells and a human pulmonary epithelial cell line, and impaired virus-induced enhancement of interleukin 6 (IL-6) and tumor necrosis factor alpha (TNF-α) levels.
Journal ArticleDOI
Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories
TL;DR: Grcarma as discussed by the authors is a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules and is a cross-platform, Perl/Tk-based front-end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user-friendly and intuitive design.
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Charge distribution and imperfect amphipathicity affect pore formation by antimicrobial peptides.
Maja Mihajlovic,Themis Lazaridis +1 more
TL;DR: These results suggest that charged residues within the N-terminal half are important for toroidal pore formation in melittin and MG-H2 mutants.
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Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain
TL;DR: The present MD results support a multisite model for the mechanism of receptor-channel modulation by anesthetics for isoflurane binding sites in the nicotinic acetylcholine receptor and the proton gated ion channel from Gloebacter violaceus.
References
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Journal ArticleDOI
Generalized Gradient Approximation Made Simple
TL;DR: A simple derivation of a simple GGA is presented, in which all parameters (other than those in LSD) are fundamental constants, and only general features of the detailed construction underlying the Perdew-Wang 1991 (PW91) GGA are invoked.
Journal ArticleDOI
Self-Consistent Equations Including Exchange and Correlation Effects
Walter Kohn,L. J. Sham +1 more
TL;DR: In this paper, the Hartree and Hartree-Fock equations are applied to a uniform electron gas, where the exchange and correlation portions of the chemical potential of the gas are used as additional effective potentials.
Journal ArticleDOI
VMD: Visual molecular dynamics
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
Journal ArticleDOI
Density-functional exchange-energy approximation with correct asymptotic behavior.
TL;DR: This work reports a gradient-corrected exchange-energy functional, containing only one parameter, that fits the exact Hartree-Fock exchange energies of a wide variety of atomic systems with remarkable accuracy, surpassing the performance of previous functionals containing two parameters or more.
Fast parallel algorithms for short-range molecular dynamics
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
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