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Unique identifier OMICS_24509

Publication for RATTLE

RATTLE citations


Transition state based ST6Gal I inhibitors: Mimicking the phosphodiester linkage with a triazole or carbamate through an enthalpy entropy compensation

Sci Rep
PMCID: 5663928
PMID: 29089525
DOI: 10.1038/s41598-017-14560-0

[…] e Mesh Ewald method. The van der Waals forces were treated with a cut-off of 12 Å and a smoothening function between 10 and 12 Å. All of the covalent bonds involving hydrogen were kept rigid with the RATTLE algorithm. The integration time step was set to 1.0 fs, 2.0 fs and 4.0 fs for bonded, non-bonded and long-range electrostatics, respectively.Equilibrium simulations for all human ST6Gal I-inhib […]


Structure and application of antifreeze proteins from Antarctic bacteria

Microb Cell Fact
PMCID: 5547475
PMID: 28784139
DOI: 10.1186/s12934-017-0737-2

[…] and Langevin piston [] were used to maintain a constant temperature of 225 K and a constant pressure of 1 atm. The equations of motion were integrated with a 2.0 fs time step along with SETTLE [] and RATTLE algorithms [] to constrain the geometry of the water molecules and the length of covalent bonds to hydrogen atoms. Non-bonded energies were calculated using particle-mesh Ewald full electrostat […]


STIM1 activates CRAC channels through rotation of the pore helix to open a hydrophobic gate

Nat Commun
PMCID: 5321763
PMID: 28220789
DOI: 10.1038/ncomms14512

[…] ation and damping timescale of 100 fs and 50 fs, respectively, with a Langevin dynamics damping coefficient of 1 ps−1 for temperature control. All bonds with hydrogen were constrained using the SHAKE/RATTLE algorithms. Nonbonded interactions were calculated using particle mesh Ewald (PME) with a 12 Å Lennard-Jones cutoff, a switch distance at 10 Å, and pair-list distance set at 16 Å. All four syst […]


A selectivity filter at the intracellular end of the acid sensing ion channel pore

PMCID: 5449180
PMID: 28498103
DOI: 10.7554/eLife.24630.015

[…] onstant pressure (1 atm) with a Langevin piston, (; ) with fixed lateral area ratio (1:1), and constant temperature using a Nosé-Hoover thermostat (; ), All bonds to H atoms were maintained using the RATTLE algorithm (). Electrostatic interactions were computed using Particle Mesh Ewald with grid spacing of 1.5 Å and 6th order B-spline for mesh interpolation. Non-bonded pair lists were updated eve […]


Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1

PMCID: 5550277
PMID: 28742020
DOI: 10.7554/eLife.25235.016
call_split See protocol

[…] for short-range nonbonded interactions was 10.0 Å; long-range electrostatics was calculated using the particle-mesh Ewald method (). All bonds involving hydrogen in the protein were constrained using RATTLE (), while the geometries of water molecules were maintained using SETTLE (). The resulting equilibrated structure was employed as the initial state for production simulations, carried out on th […]


Understanding the role of dynamics in the iron sulfur cluster molecular machine

Biochim Biophys Acta
PMCID: 5176006
PMID: 27474202
DOI: 10.1016/j.bbagen.2016.07.020
call_split See protocol

[…] ed for atom pair interactions. The long-range electrostatic interactions were computed by means of the particle mesh Ewald (PME) method using a 1.0 Å grid spacing in periodic boundary conditions. The RATTLE algorithm was applied to constrain bonds involving hydrogen atoms, and thus a 2 fs time step could be used. All the systems were simulated with NAMD (v. 2.9), using the ff99SBildn Amber force […]


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RATTLE institution(s)
Department of Chemistry, Stanford University, Stanford, CA, USA
RATTLE funding source(s)
Supported by National Institutes of Health Grant GM-26626.

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