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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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Self-assembly of β-sheet forming peptides into chiral fibrillar aggregates
Giovanni Bellesia,Joan-Emma Shea +1 more
TL;DR: In this paper, the authors introduce a coarse-grained model to investigate the self-assembly of β-sheet forming peptides, which retains most of the peptide backbone degrees of freedom as well as one interaction center describing the side chains.
Journal ArticleDOI
Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors.
TL;DR: Ligand binding assays, crystallographic analysis, and all atom MD simulations revealed numerous interdomain contacts, which stabilize the agonist‐bound closed‐cleft conformation, and a novel twisting motion for the loop 1 helix that is unique in NR3 subunits.
Journal ArticleDOI
Structural insight into selectivity and resistance profiles of ROS1 tyrosine kinase inhibitors
Monika A. Davare,Nadeem A. Vellore,Jacob P. Wagner,Christopher A. Eide,Christopher A. Eide,James R. Goodman,Alexander Drilon,Michael W. Deininger,Thomas O'Hare,Brian J. Druker,Brian J. Druker +10 more
TL;DR: In this article, the sensitivity and selectivity of seven ROS1 and/or ALK inhibitors at various levels of clinical development were analyzed. And the authors showed that the ROS1-selective inhibitors retain efficacy against the recently reported CD74-ROS1(G2032R) mutant whereas the dual ROS1/ALK inhibitors are ineffective.
Journal ArticleDOI
Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method.
TL;DR: eABF does not directly bias the collective coordinates of interest, but rather fictitious variables that are harmonically coupled to them, making it easily applicable to a wider range of problems than ABF, and it converges to the physical free energy surface faster than standard ABF for a wide range of parameters.
Journal ArticleDOI
Redox-induced activation of the proton pump in the respiratory complex I
Vivek Sharma,Galina Belevich,Ana P. Gamiz-Hernandez,Tomasz Róg,Ilpo Vattulainen,Ilpo Vattulainen,Marina Verkhovskaya,Mårten Wikström,Gerhard Hummer,Ville R. I. Kaila +9 more
TL;DR: Simulations indicate that reduction of Q leads to local charge redistributions that trigger conformational changes via an array of alternating charged residues in the membrane domain, nearly 40 Å away, and suggest that the proton pumping in complex I is activated by a unique combination of electrostatic and conformational transitions.
References
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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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