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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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Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.
Melissa R. Landon,Rommie E. Amaro,Riccardo Baron,Chi Ho Ngan,David Ozonoff,J. Andrew McCammon,Sandor Vajda +6 more
TL;DR: The synergistic application of extended explicit solvent molecular dynamics (MD) and computational solvent mapping (CS‐Map) to identify putative ‘hot spots’ within flexible binding regions of N1 neuraminidase provides further support for the feasibility of developing high‐affinity inhibitors capable of binding these regions.
Journal ArticleDOI
OGOLEM: Global cluster structure optimisation for arbitrary mixtures of flexible molecules. A multiscaling, object-oriented approach
TL;DR: OGOLEM as discussed by the authors is a program suite that is universal by design, both in cluster composition (including arbitrarily heterogeneous clusters of complicated molecules) and in its interfaces to force calculation backends.
Journal ArticleDOI
Graphene-Induced Pore Formation on Cell Membranes
Guangxin Duan,Yuanzhao Zhang,Binquan Luan,Jeffrey K. Weber,Royce W. Zhou,Zaixing Yang,Lin Zhao,Jiaying Xu,Judong Luo,Judong Luo,Ruhong Zhou,Ruhong Zhou,Ruhong Zhou +12 more
TL;DR: It is demonstrated that graphene nanosheets (both pristine and oxidized) can produce holes (pores) in the membranes of A549 and Raw264.7 cells, substantially reducing cell viability.
Journal ArticleDOI
Sampling protein motion and solvent effect during ligand binding
Vittorio Limongelli,Luciana Marinelli,Sandro Cosconati,Concettina La Motta,Stefania Sartini,L. Mugnaini,Federico Da Settimo,Ettore Novellino,Michele Parrinello +8 more
TL;DR: The mechanism of binding of a new series of potent inhibitors of Adenosine Deaminase is developed and revealed and the lowest energy binding modes of the most potent compound of the series, 4-decyl-pyrazolo[1,5-a]pyrimidin-7-one are identified.
Journal ArticleDOI
PEGylated reduced graphene oxide as a superior ssRNA delivery system
Liming Zhang,Liming Zhang,Liming Zhang,Zunliang Wang,Zhuoxuan Lu,Zhuoxuan Lu,He Shen,Jie Huang,Qinghuan Zhao,Min Liu,Nongyue He,Nongyue He,Zhijun Zhang +12 more
TL;DR: It is demonstrated that PEG-RGO exhibits superior ssRNA loading and delivery capability, compared to the widely studied PEGylated graphene oxide (PEG-GO).
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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