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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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Journal ArticleDOI
Catch-bond mechanism of the bacterial adhesin FimH
Maximilian M. Sauer,Roman P. Jakob,Jonathan Eras,Sefer Baday,Sefer Baday,Deniz Eriş,Giulio Navarra,Simon Bernèche,Simon Bernèche,Beat Ernst,Timm Maier,Rudi Glockshuber +11 more
TL;DR: A three-state mechanism of FimH catch-bond formation is revealed based on crystal structures of all states, kinetic analysis of ligand interaction and molecular dynamics simulations, which demonstrates that rapid ligand dissociation from FIMH supports motility of piliated E. coli on mannosylated surfaces in the absence of shear force.
Journal ArticleDOI
High-resolution cryo-EM analysis of the yeast ATP synthase in a lipid membrane
Anurag P. Srivastava,Min Luo,Wenchang Zhou,Jindrich Symersky,Dongyang Bai,Melissa G. Chambers,José D. Faraldo-Gómez,Maofu Liao,David M. Mueller +8 more
TL;DR: The mitochondrial adenosine triphosphate (ATP) synthase is the enzyme responsible for the synthesis of more than 90% of the ATP produced by mammalian cells under aerobic conditions and the chemiosmotic mechanism, proposed by Peter Mitchell, states that the enzyme transduces the energy of a proton gradient into the major energy currency of the cell, ATP.
Journal ArticleDOI
Single-molecule detection with a millimetre-sized transistor.
Eleonora Macchia,Kyriaki Manoli,Brigitte Holzer,Cinzia Di Franco,Matteo Ghittorelli,Fabrizio Torricelli,Domenico Alberga,Giuseppe Felice Mangiatordi,Gerardo Palazzo,Gaetano Scamarcio,Luisa Torsi,Luisa Torsi +11 more
TL;DR: A millimetre-sized field effect transistor capable of selective single-molecule Immunoglobulin-G detection is demonstrated and can revolutionize the current approach to protein detection.
Journal ArticleDOI
Instantaneous ion configurations in the K+ ion channel selectivity filter revealed by 2D IR spectroscopy.
Huong T. Kratochvil,Joshua K. Carr,Kimberly Matulef,Alvin W. Annen,Hui Li,Michał Maj,Jared Ostmeyer,Arnaldo L. Serrano,H. Raghuraman,Sean D. Moran,James L. Skinner,Eduardo Perozo,Benoît Roux,Francis I. Valiyaveetil,Martin T. Zanni +14 more
TL;DR: 2D IR spectra of a semisynthetic KcsA channel with site-specific heavy isotope labels in the selectivity filter provide an instantaneous snapshot of the multi-ion configurations and structural distributions that occur spontaneously in the filter.
Journal ArticleDOI
Pore opening and closing of a pentameric ligand-gated ion channel
Fangqiang Zhu,Gerhard Hummer +1 more
TL;DR: It is concluded that the pore of the isolated GLIC transmembrane domain closes spontaneously from the free energy profile of the gating transition and from unrestrained simulations, which conclude that strong interactions of this short and conserved loop with the extracellular domain are crucial to couple ligand binding to channel opening.
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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