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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
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Drug repurposing for coronavirus (COVID-19): in silico screening of known drugs against coronavirus 3CL hydrolase and protease enzymes.
TL;DR: An effort was made to identify commercially available drugs in order to repurpose them against coronavirus by the means of structure-based virtual screening and the results showed four potential inhibitors against Mpro enzyme, two available drugs and two novel drug-like compounds.
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Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.
TL;DR: Application of the CHARMM36 model to a collection of canonical and noncanonical RNA molecules reveals overall improved agreement with a range of experimental observables as compared to CHARMM27, and indicates the sensitivity of the conformational heterogeneity of RNA to the orientation of the 2′‐hydroxyl moiety to support a model whereby the 2‐Hydroxyl can enhance the probability of conformational transitions in RNA.
Journal ArticleDOI
Transparent, Adhesive, and Conductive Hydrogel for Soft Bioelectronics Based on Light-Transmitting Polydopamine-Doped Polypyrrole Nanofibrils
TL;DR: A transparent, conductive, stretchable, and self-adhesive hydrogel by in situ formation of polydopamine (PDA)-doped polypyrrole (PPy) nanofibrils in the polymer network was reported in this paper.
Journal ArticleDOI
ALK mutations confer differential oncogenic activation and sensitivity to ALK inhibition therapy in neuroblastoma
Scott C. Bresler,Daniel A. Weiser,Daniel A. Weiser,Peter J. Huwe,Jin H. Park,Kateryna Krytska,Hannah T. Ryles,Marci Laudenslager,Eric F. Rappaport,Andrew Wood,Patrick McGrady,Michael D. Hogarty,Michael D. Hogarty,Wendy B. London,Wendy B. London,Ravi Radhakrishnan,Mark A. Lemmon,Yael P. Mosse,Yael P. Mosse +18 more
TL;DR: These studies identify ALK genomic status as a clinically important therapeutic stratification tool in neuroblastoma and will allow tailoring of ALK-targeted therapy to specific mutations, and identify oncogenic (constitutively activating) from nononcogenic mutations.
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CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
TL;DR: CHARMM-GUI Martini Maker is developed, which supports 82 lipid types and different flavors of the Martini force field, and is expected to be a useful tool for modeling large, complicated biomolecular systems in a user-friendly way.
References
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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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