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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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Journal ArticleDOI
Molecular signatures of ribosomal evolution
TL;DR: It is proposed that the ribosomal signatures are remnants of an evolutionary-phase transition that occurred as the cell lineages began to coalesce and so should be reflected in corresponding signatures throughout the fabric of the cell and its genome.
Journal ArticleDOI
Structural Basis for Calmodulin as a Dynamic Calcium Sensor
Miao Zhang,Cameron F. Abrams,Liping Wang,Anthony Gizzi,Liping He,Ruihe Lin,Yuan Chen,Patrick J. Loll,John M. Pascal,Ji-Fang Zhang +9 more
TL;DR: This work takes advantage of two splice variants of SK2 channels, which are activated by Ca(2+)-bound calmodulin but show different sensitivity to Ca( 2+) for their activation, and adopts drastically different conformations with different affinities forCa(2+) at its C-lobe.
Journal ArticleDOI
A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion.
Sam J. B. Mallinson,Melodie M. Machovina,Melodie M. Machovina,Rodrigo L. Silveira,Rodrigo L. Silveira,Marc Garcia-Borràs,Nathan M. Gallup,Nathan M. Gallup,Christopher W. Johnson,Mark D. Allen,Munir S. Skaf,Michael F. Crowley,Ellen L. Neidle,Kendall N. Houk,Gregg T. Beckham,Jennifer L. DuBois,John McGeehan +16 more
TL;DR: The authors present the structures of GcoA and GcoB, a cytochrome P450-reductase pair that catalyzes aryl-O-demethylations and show that G coA displays broad substrate specificity, which is of interest for biotechnology applications.
Journal ArticleDOI
Conformational transitions of the serotonin 5-HT3receptor.
Lucie Polovinkin,Ghérici Hassaine,Jonathan Perot,Emmanuelle Neumann,Anders A. Jensen,Solène N Lefebvre,Pierre-Jean Corringer,Jacques Neyton,Christophe Chipot,Christophe Chipot,François Dehez,François Dehez,Guy Schoehn,Hugues Nury +13 more
TL;DR: Cryo-electron microscopy structures of the full-length mouse 5-HT3 receptor in complex with the anti-emetic drug tropisetron, with serotonin, and with serotonin and a positive allosteric modulator are reported, deepening understanding of the gating mechanism of pLGICs and capture ligand binding in unprecedented detail.
Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic
TL;DR: The simulations suggest that gating movements of the α7 receptor may involve relatively small structural changes within the ligand-binding domain, implying that the gating transition is energy-efficient and can be easily modulated by agonist binding/unbinding.
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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