Open AccessBook
Scalable Molecular Dynamics with NAMD
About:
The article was published on 2012-12-14 and is currently open access. It has received 13375 citations till now.read more
Citations
More filters
Journal ArticleDOI
A Gain-of-Function Mutation of Arabidopsis Lipid Transfer Protein 5 Disturbs Pollen Tube Tip Growth and Fertilization
TL;DR: Pollen tube growth defects resulted in defects in polar tip growth of pollen tubes and thereby decreased seed set, suggesting that mutant ltp5-1 acts as a dominant-active form of wild-type LTP5 in pollen tube growth.
Journal ArticleDOI
Mutual adaptation of a membrane protein and its lipid bilayer during conformational changes
Yonathan Sonntag,Maria Musgaard,Maria Musgaard,Claus Olesen,Claus Olesen,Birgit Schiøtt,Birgit Schiøtt,Jesper V. Møller,Jesper V. Møller,Poul Nissen,Poul Nissen,Lea Thøgersen,Lea Thøgersen +12 more
TL;DR: It is found that SERCA adapts to membranes of different hydrophobic thicknesses by inducing local deformations in the lipid bilayers and by undergoing small rearrangements of the amino-acid side chains and helix tilts that allow smooth transitions through large conformational changes associated with the transport cycle of SERCA.
Journal ArticleDOI
Rhomboid protease dynamics and lipid interactions.
TL;DR: In this article, the authors examined the molecular dynamics of wild-type and mutant GlpG in different membrane environments and concluded that the L1 loop has an important regulatory role in proteolysis.
Journal ArticleDOI
Quantitative Characterization of the Binding and Unbinding of Millimolar Drug Fragments with Molecular Dynamics Simulations.
TL;DR: Long time scale fragment binding simulations of sufficient length are performed, allowing the binding affinities, on- and off-rates, and relative occupancies of alternative binding sites and alternative poses within each binding site to be estimated, thereby illustrating the potential of long time scale MD as a quantitative tool for fragment-based drug discovery.
Journal ArticleDOI
Molecular mechanism of Aurora A kinase autophosphorylation and its allosteric activation by TPX2
Adelajda Zorba,Vanessa Buosi,Steffen Kutter,Nadja Kern,Francesco Pontiggia,Young-Jin Cho,Dorothee Kern +6 more
TL;DR: While autophosphorylation is the key regulatory mechanism in the centrosomes in the early stages of mitosis, allosteric activation by TPX2 of dephosphorylated Aurora A could be at play in the spindle microtubules.
References
More filters
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.
Related Papers (5)
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
Alexander D. MacKerell,D. Bashford,M. Bellott,Roland L. Dunbrack,Jeffrey D. Evanseck,Martin J. Field,Stefan Fischer,Jiali Gao,H. Guo,S. Ha,Diane Joseph-McCarthy,L. Kuchnir,K. Kuczera,F. T. K. Lau,C. Mattos,Stephen W. Michnick,Thien H. Ngo,D. T. Nguyen,B. Prodhom,W. E. Reiher,Benoît Roux,M. Schlenkrich,Jeremy C. Smith,Roland H. Stote,John E. Straub,Masakatsu Watanabe,J. Wiórkiewicz-Kuczera,D. Yin,Martin Karplus +28 more