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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
Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field
Hui Li,Van A. Ngo,Mauricio Chagas da Silva,Dennis R. Salahub,Karen M. Callahan,Benoît Roux,Sergei Y. Noskov +6 more
TL;DR: This study presents a systematic effort to optimize the parameters of a polarizable force field based on classical Drude oscillators to accurately represent the interactions between ions and coordinating amino-acid residues for a set of 30 biologically important proteins, offering a powerful avenue to study the roles of the ions in soluble and membrane transport proteins.
Journal ArticleDOI
Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene
TL;DR: Investigation of how interactions of single-stranded DNA and a graphene membrane can be controlled by electrically biasing the membrane suggests electric charge on graphene can force a DNA homopolymer to adopt a range of strikingly different conformations.
Journal ArticleDOI
Insights into the assembly and activation of the microtubule nucleator γ-TuRC
Peng Liu,Erik Zupa,Annett Neuner,Anna Böhler,Justus Loerke,Dirk Flemming,Thomas Ruppert,Till Rudack,Christoph Peter,Christian M. T. Spahn,Oliver J. Gruss,Stefan Pfeffer,Elmar Schiebel +12 more
TL;DR: The cryo-electron microscopy reconstructions of the γ-tubulin ring complex from Xenopus laevis provides insights into the molecular organization of the complex, and shows that actin is a structural component that is functionally relevant to microtubule nucleation.
Journal ArticleDOI
Influence of the Shape of Nanostructured Metal Surfaces on Adsorption of Single Peptide Molecules in Aqueous Solution
TL;DR: The proposed adsorption mechanism is supported and critically evaluated by earlier sequence data from phage display, dissociation constants of small proteins as a function of nanoparticle size, and observed shapes of peptide-stabilized nanoparticles.
Journal ArticleDOI
Autonomous Generation and Loading of DNA Guides by Bacterial Argonaute
Daan C. Swarts,Malwina Szczepaniak,Gang Sheng,Stanley D. Chandradoss,Yifan Zhu,Elizabeth M. Timmers,Yong Zhang,Hongtu Zhao,Jizhong Lou,Yanli Wang,Chirlmin Joo,John van der Oost +11 more
TL;DR: It is demonstrated that guide-free Argonaute from Thermus thermophilus (TtAgo) can degrade double-stranded DNA (dsDNA), thereby generating small dsDNA fragments that subsequently are loaded onto pAgo and can independently generate and selectively load functional DNA guides.
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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