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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
Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution
TL;DR: The structural model supports the concept of "conformer selection", which emphasizes the conformational flexibility of N-glycans in protein-glycan interactions, and reduces the number of major conformers to two and from five to four upon the introduction of bisecting GlcNAc and core fucosylation, respectively.
Journal ArticleDOI
Molecular dynamics simulations in membrane-based water treatment processes: A systematic overview
TL;DR: The theoretical foundations of classical MD are described together with the results that are obtainable from MDM simulations and the authors suggest the further use of MDM for prospective research areas pertaining to membrane-based water treatment processes.
Journal ArticleDOI
Molecular Mechanism of Peroxisome Proliferator-Activated Receptor α Activation by WY14643: a New Mode of Ligand Recognition and Receptor Stabilization
Amanda Bernardes,Paulo C. T. Souza,João R. C. Muniz,Clarisse G. Ricci,Stephen D. Ayers,Nili M Parekh,Andre S. Godoy,Daniela B. B. Trivella,Peter S. Reinach,Paul Webb,Munir S. Skaf,Igor Polikarpov +11 more
TL;DR: The unique binding mode of WY14643 reveals a new pattern of nuclear receptor ligand recognition and suggests a novel basis for ligand design, offering clues for improving the binding affinity and selectivity of ligand.
Journal ArticleDOI
Structural insights into Ca2+-activated long-range allosteric channel gating of RyR1
Risheng Wei,Xue Wang,Yan Zhang,Saptarshi Mukherjee,Lei Zhang,Qiang Chen,Xinrui Huang,Shan Jing,Congcong Liu,Shuang Li,Guangyu Wang,Yaofang Xu,Sujie Zhu,Alan J. Williams,Fei Sun,Chang-Cheng Yin +15 more
TL;DR: The characterization of a Ca2+-activated open-state RyR1 structure by cryo-electron microscopy provides structural insights into the molecular mechanisms of channel gating and regulation of RyRs and sheds light on structural basis for channel-gating and ion selectivity mechanisms for the six-transmembrane-helix cation channel family.
Journal ArticleDOI
Molecular Basis of Ligand Dissociation in β-Adrenergic Receptors
TL;DR: The steered molecular dynamics simulation method is used to describe, in atomic detail, the unbinding process of two inverse agonists, which have been recently co-crystallized with β1 and β2ARs subtypes, along four different channels and suggests the presence of secondary binding sites located in the extracellular loops 2 and 3 and transmembrane helix 7.
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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