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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
Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain.
Carina Frauer,Thomas Hoffmann,Thomas Hoffmann,Sebastian Bultmann,Sebastian Bultmann,Valentina Casa,M. Cristina Cardoso,Iris Antes,Iris Antes,Heinrich Leonhardt,Heinrich Leonhardt +10 more
TL;DR: The SRA domain of Uhrf1, an essential factor in DNA maintenance methylation, binds 5hmC and 5-methylcytosine containing substrates with similar affinity and stabilizes the flipped base by hydrogen bond formation with the hydroxyl group.
Journal ArticleDOI
The human IgM pentamer is a mushroom-shaped molecule with a flexural bias
TL;DR: A homology-based structural model of the IgM pentamer using the recently obtained crystallographic structure of IgE Fc, which has this additional Ig domain under the constraint that all of the cysteine residues known to form disulfide bridges both within each monomer and between monomers are bonded together is constructed.
Journal ArticleDOI
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
Christopher D. Wassman,Roberta Baronio,Özlem Demir,Özlem Demir,Brad D. Wallentine,Chiung-Kuang Chen,Linda V. Hall,Faezeh Salehi,Dawei Lin,Benjamin P. Chung,G. Wesley Hatfield,A. Richard Chamberlin,Hartmut Luecke,Richard H. Lathrop,Peter K. Kaiser,Rommie E. Amaro +15 more
TL;DR: In this paper, a transiently open binding pocket between loop L1 and sheet S3 of the p53 core domain was identified as a target for pharmaceutical reactivation of p53 mutants.
Journal ArticleDOI
CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work
Hiroo Kenzaki,Nobuyasu Koga,Naoto Hori,Ryo Kanada,Wenfei Li,Wenfei Li,Kei-ichi Okazaki,Xin-Qiu Yao,Shoji Takada +8 more
TL;DR: For simulating proteins at work in millisecond time scale or longer, a coarse-grained molecular dynamics method and software, CafeMol, is developed that has various and flexible means to "switch" the energy functions that induce active motions of the proteins.
Journal ArticleDOI
Controlling the direction of rectification in a molecular diode
Li Yuan,Nisachol Nerngchamnong,Liang Cao,Hicham Hamoudi,Enrique del Barco,Max Roemer,Ravi K. Sriramula,Damien Thompson,Christian A. Nijhuis +8 more
TL;DR: This work shows that non-covalent contacts between the active molecular component and the electrodes allow for robust coupling with minimal energy broadening of the molecular level, precisely what is required to maximize the rectification ratio of a molecular diode.
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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