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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
Transmission Coefficients, Committors, and Solvent Coordinates in Ion-Pair Dissociation.
TL;DR: For NaCl dissociation in TIP3P water, it is shown that Recrossing persists even when the 1/2-committor surface itself is used as the dividing surface, providing evidence that recrossing cannot be fully eliminated from the dynamics for any configurational coordinate.
Journal ArticleDOI
A novel mechano-enzymatic cleavage mechanism underlies transthyretin amyloidogenesis
Julien Marcoux,Julien Marcoux,Palma Mangione,Palma Mangione,Riccardo Porcari,Matteo T. Degiacomi,Guglielmo Verona,Guglielmo Verona,Graham W. Taylor,Sofia Giorgetti,Sara Raimondi,Sarah Sanglier-Cianférani,Justin L. P. Benesch,Ciro Cecconi,Mohsin M. Naqvi,Julian D. Gillmore,Philip N. Hawkins,Monica Stoppini,Carol V. Robinson,Mark B. Pepys,Vittorio Bellotti,Vittorio Bellotti +21 more
TL;DR: The mechanism of cleavage and release of the 49–127 fragment from the prototypic S52P variant is investigated, and it is proposed that a mechano‐enzymatic mechanism mediates transthyretin amyloid fibrillogenesis in vivo.
Journal ArticleDOI
Theoretical Characterization of Substrate Access/Exit Channels in the Human Cytochrome P450 3A4 Enzyme: Involvement of Phenylalanine Residues in the Gating Mechanism
TL;DR: It is argued that product exit preferences in P450s are regulated by protein−substrate specificity, and there is more than just one access/exit channel in CYP3A4.
Journal ArticleDOI
Parallel damage in mitochondria and lysosomes is an efficient way to photoinduce cell death.
Waleska Kerllen Martins,Nayra Fernandes Santos,Cleidiane de Sousa Rocha,Isabel O. L. Bacellar,Tayana Mazin Tsubone,Ana Cláudia Viotto,Adriana Yamaguti Matsukuma,Aline B. de P. Abrantes,Paulo Siani,Luís G. Dias,Mauricio S. Baptista +10 more
TL;DR: It is shown that the parallel damage in mitochondria and lysosomes activates and inhibits mitophagy, leading to a late and more efficient cell death, offering significant advantage (2 orders of magnitude) over photosensitizers that cause unspecific oxidative stress.
Journal ArticleDOI
LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor.
TL;DR: LARMD provides a user-friendly online protocol to study the dynamic property of protein and to design new ligand or site-directed mutagenesis, which plays a vital role in the treatment of inflammatory diseases and many types of cancers in clinical practice.
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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