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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
Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins
Giorgio Schirò,Giorgio Schirò,Yann Fichou,Francois Xavier Gallat,Kathleen Wood,Frank Gabel,Frank Gabel,Martine Moulin,Michael Härtlein,Matthias Heyden,Jacques-Philippe Colletier,Jacques-Philippe Colletier,Andrea Orecchini,Alessandro Paciaroni,Joachim Wuttke,Douglas J. Tobias,Martin Weik,Martin Weik +17 more
TL;DR: The notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity is generalized.
Journal ArticleDOI
Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein.
Canan Atilgan,Ali Rana Atilgan +1 more
TL;DR: P perturbation-response scanning is introduced for the analysis of remote control strategies utilized and it is found that the cap residues involved in iron release are made to operate coherently, facilitating release of the ion.
Journal ArticleDOI
High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome
Houssam Hajjoul,Houssam Hajjoul,Julien Mathon,Julien Mathon,Hubert Ranchon,Hubert Ranchon,Isabelle Goiffon,Isabelle Goiffon,Julien Mozziconacci,Benjamin Albert,Benjamin Albert,Pascal Carrivain,Jean-Marc Victor,Olivier Gadal,Olivier Gadal,Kerstin Bystricky,Kerstin Bystricky,Aurélien Bancaud,Aurélien Bancaud +18 more
TL;DR: The analysis of the amplitude of fluctuations by the Rouse model shows that yeast chromatin is highly flexible, its persistence length being qualitatively estimated to <30 nm and suggesting that it provides a consistent framework to study chromatin dynamics.
Journal ArticleDOI
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics.
TL;DR: POVME 2.0 is presented, which is an order of magnitude faster, has improved accuracy, includes a graphical user interface, and can produce volumetric density maps for improved pocket analysis.
Journal ArticleDOI
A human monoclonal antibody prevents malaria infection by targeting a new site of vulnerability on the parasite
Neville K. Kisalu,Azza H. Idris,Connor Weidle,Yevel Flores-Garcia,Barbara J. Flynn,Brandon K. Sack,Sean C. Murphy,Arne Schön,Ernesto Freire,Joseph R. Francica,Alex B. Miller,Jason Gregory,Sandra March,Hua-Xin Liao,Barton F. Haynes,Kevin Wiehe,Ashley M. Trama,Kevin O. Saunders,Morgan A. Gladden,Anthony Monroe,Mattia Bonsignori,Masaru Kanekiyo,Adam K. Wheatley,Adrian B. McDermott,S. Katie Farney,Gwo-Yu Chuang,Baoshan Zhang,Natasha Kc,Sumana Chakravarty,Peter D. Kwong,Photini Sinnis,Sangeeta N. Bhatia,Stefan H. I. Kappe,B. Kim Lee Sim,Stephen L. Hoffman,Fidel Zavala,Marie Pancera,Robert A. Seder +37 more
TL;DR: The demonstration that CIS43 is highly effective for passive prevention of malaria has potential application for use in travelers, military personnel and elimination campaigns and identifies a new and conserved site of vulnerability on PfCSP for next-generation rational vaccine design.
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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