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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
Mechanisms for the Insertion of Toxic, Fibril-like β-Amyloid Oligomers into the Membrane.
Hyunbum Jang,Laura Connelly,Fernando Teran Arce,Srinivasan Ramachandran,Bruce L. Kagan,Ratnesh Lal,Ruth Nussinov,Ruth Nussinov +7 more
TL;DR: Using explicit solvent molecular dynamics simulations, it is shown that fibril-like Aβ(17-42) (p3) oligomer is capable of penetrating the membrane and proposed that monomers and dimers may insert in (apparently on-pathway) aggregation-intermediate β-hairpin state, and may (or may not) convert to a U-shape in the bilayer.
Journal ArticleDOI
Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics
TL;DR: In this paper, the authors analyzed the charge transfer at the Bovine pancreatic trypsin inhibitor (BPTI) protein-water interface by means of ab initio Born-Oppenheimer molecular dynamics simulation of the entire protein running on graphical processing units (GPUs).
Journal ArticleDOI
Structural basis of transfer between lipoproteins by cholesteryl ester transfer protein
Lei Zhang,Feng Yan,Shengli Zhang,Dongsheng Lei,M. Arthur Charles,Giorgio Cavigiolio,Michael N. Oda,Ronald M. Krauss,Karl H. Weisgraber,Kerry-Anne Rye,Kerry-Anne Rye,Kerry-Anne Rye,Henry J. Pownall,Xiayang Qiu,Gang Ren,Gang Ren,Gang Ren +16 more
TL;DR: In this mechanistic model, the CETP lipoprotein-interacting regions form pores that connect to a hydrophobic central cavity, thereby forming a tunnel for transfer of neutral lipids from donor to acceptor lipoproteins and provide a molecular basis for analyzing mechanisms for CETP inhibition.
Journal ArticleDOI
Dynamical motions of lipids and a finite size effect in simulations of bilayers.
TL;DR: Reorientational correlation functions for the slowly relaxing phosphorus-glycerol hydrogen, phosphorus-nitrogen vectors, and more rapidly relaxing CH vectors in the aliphatic chains are equivalent for the 72 and 288 lipid simulations.
Journal ArticleDOI
Structural basis for cofilin binding and actin filament disassembly
Kotaro Tanaka,Shuichi Takeda,Kaoru Mitsuoka,Toshiro Oda,Chieko Kimura-Sakiyama,Yuichiro Maéda,Yuichiro Maéda,Akihiro Narita +7 more
TL;DR: Cofilin is a small actin-binding protein that accelerates actin turnover by disassembling actin filaments and the 3.8 Å cryo-EM structure of a cofilin-decorated actin filament is presented and mechanistic implications are discussed.
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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