Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters

Bowers,; Chow,; Xu, Jun; Dror,; Eastwood,; Gregersen,; Klepeis,; Kolossvary,; Moraes,; Sacerdoti,; Salmon,; Shan, Shan; Shaw,

doi:10.1109/sc.2006.54

Cited by 1,897 publications

(1,729 citation statements)

References 46 publications

(59 reference statements)

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“…19 Conformations were saved every 2 ps during the 1.2 µs simulation to obtain an ensemble of 6 × 10 5 conformations, which represent both the overall and internal motions of ubiquitin.…”

Section: Methodsmentioning

confidence: 99%

Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins

et al. 2008

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A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 µs explicit solvent MD simulation of the protein ubiquitin are compared with previously determined backbone order parameters derived from NMR relaxation experiments [Tjandra, N.; Feller, S. E.; Pastor, R. W.; Bax, A. J. Am. Chem. Soc. 1995, 117, 12562-12566]. The simulation reveals fluctuations in three loop regions that occur on time scales comparable to or longer than that of the overall rotational diffusion of ubiquitin and whose effects would not be apparent in experimentally derived order parameters. A coupled analysis of internal and overall motion yields simulated order parameters substantially closer to the experimentally determined values than is the case for a conventional analysis of internal motion alone. Improved agreement between simulation and experiment also is encouraging from the viewpoint of assessing the accuracy of long MD simulations.

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“…19 Conformations were saved every 2 ps during the 1.2 µs simulation to obtain an ensemble of 6 × 10 5 conformations, which represent both the overall and internal motions of ubiquitin.…”

Section: Methodsmentioning

confidence: 99%

Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins

et al. 2008

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“…This can be done during post processing on the trajectory file, much like a conventional analysis tool, or on-the-fly during the simulation. Other software is available for analyzing existing trajectories [7,20,21,22,23,24] or for biasing MD simulations [15,9,25,26,27,7,6]. PLUMED 2, however, is the only code we know of that allows users to do both sets of tasks with a single syntax.…”

Section: Plumed 2 Overviewmentioning

confidence: 99%

PLUMED 2: New feathers for an old bird

Tribello

Bonomi

Branduardi

et al. 2014

Computer Physics Communications

2,909

2,841

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Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardwares, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here -a complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

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“…MD simulations of TRPM8/12 and TRPM8/21 complexes were set and run using Desmond MD system [48][49][50] . The simulated environment was built using the system builder utility, with the structures …”

Section: Molecular Dynamics Simulationmentioning

confidence: 99%

Tryptamine-Based Derivatives as Transient Receptor Potential Melastatin Type 8 (TRPM8) Channel Modulators

et al. 2016

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Pharmacological modulation of the transient receptor potential melastatin type 8 (TRPM8) is currently under investigation as a new approach mainly for the treatment of pain. In this study, a series of N-substituted tryptamines was prepared to explore the structural requirements determining TRPM8 modulation. As a result of a fluorescence-based screening assay, we identified two compounds acting as an activator (2-(1H-indol-3-yl)-N-(4-phenoxybenzyl) ethanamine, compound 21) or an inhibitor (N,N-dibenzyl-2-(1H-indol-3-yl) ethanamine, compound 12) of calcium influx in HEK293 cells. In patch-clamp recordings, compound 21 displayed a significantly higher potency (EC 50 = 40±4 µM) and a similar efficacy when compared to menthol; by contrast, compound 12 produced a concentrationdependent inhibition of menthol-induced TRPM8 currents (IC 50 = 367±24 nM). Molecular modelling studies using a homology model of a single TRPM8 subunit identified a putative binding site located between the VSD and the TRP box, disclosing two different binding modes for the agonist and the antagonist.

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Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters

Cited by 1,897 publications

References 46 publications

Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins

Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins

PLUMED 2: New feathers for an old bird

Tryptamine-Based Derivatives as Transient Receptor Potential Melastatin Type 8 (TRPM8) Channel Modulators

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