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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
Ultrastable cellulosome-adhesion complex tightens under load.
Constantin Schoeler,Klara H. Malinowska,Rafael C. Bernardi,Lukas F. Milles,Markus A. Jobst,Ellis Durner,Wolfgang Ott,Daniel B. Fried,Edward A. Bayer,Klaus Schulten,Hermann E. Gaub,Michael A. Nash +11 more
TL;DR: The ligand–receptor complex responsible for substrate anchoring in the Ruminococcus flavefaciens cellulosome is characterized using single-molecule force spectroscopy and steered molecular dynamics simulations and it is suggested that certain network components serve as mechanical effectors for maintaining network integrity.
Arginine and the Hofmeister Series: The Role of Ion–Ion Interactions in Protein Aggregation Suppression
TL;DR: An in depth analysis of the role the counterion plays in the aggregation suppression behavior of arginine is reported, and it appears that dihydrogen phosphate, sulfate, and citrate have strong attractive interactions with the guanidinium group of Arginine, which seems to contribute to the superior aggregation suppression ability of those salt forms by bridging together multipleArginine molecules into clusters.
Journal ArticleDOI
Fusion pore formation and expansion induced by Ca2+ and synaptotagmin 1
Ying Lai,Jiajie Diao,Yanxin Liu,Yuji Ishitsuka,Zengliu Su,Klaus Schulten,Taekjip Ha,Taekjip Ha,Yeon-Kyun Shin,Yeon-Kyun Shin +9 more
TL;DR: Using methods detecting the intervesicular mixing of small and large cargoes at a single-vesicle level, it is found that the neuronal SNARE complexes have the capacity to drive membrane hemifusion, but efficient fusion pore formation and expansion require synaptotagmin 1 and Ca2+.
Journal ArticleDOI
Exploring the Binding Mechanism of Metabotropic Glutamate Receptor 5 Negative Allosteric Modulators in Clinical Trials by Molecular Dynamics Simulations
Tingting Fu,Tingting Fu,Guoxun Zheng,Guoxun Zheng,Gao Tu,Gao Tu,Fengyuan Yang,Fengyuan Yang,Yu Zong Chen,Xiaojun Yao,Xiaofeng Li,Xiaofeng Li,Weiwei Xue,Feng Zhu,Feng Zhu +14 more
TL;DR: This comprehensive study presented a better understanding of mGlu5 receptor NAMs binding mechanism, which would be further used as a useful framework to assess and discover novel lead scaffolds for N AMs.
Journal ArticleDOI
Nitric oxide conduction by the brain aquaporin AQP4
Yi Wang,Emad Tajkhorshid +1 more
TL;DR: Simulation techniques are employed to examine the permeability of the brain aquaporin AQP4 to NO and O2 and to describe energetics and pathways associated with these phenomena, finding the low barrier against gas permeation through AQP 4 indicates that it can participate in gas conduction across the cellular membrane.
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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