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ShareScore release 0.9.0
Dataset results
8 results for “Martini 3”
Scaling protein-water interactions in the Martini 3 coarse-grained force field to simulate transmembrane helix dimers in different lipid environments
<p>This dataset contains molecular dynamics (MD) trajectories used for preparation of the following manuscript: <br> "Scaling protein-water interactions in the Martini 3 coarse-grained force field to simulate transmembrane helix dimers in different lipid environments". </p>
MD simulations of the Sec61/TRAP complex with the Martini 3 force field
<p>Simulation data for the Sec61/TRAP complex, the Sec61 complex, and the TRAP complex in a POPC membrane. Simulations are performed using GROMACS and with the coarse-grained Martini 3 force fields. The proteins are kept restrained in the simulations. The uploaded trajectories (xtc) contain the coordinates stored every 10 ns of the 20-µs-long simulations. The output energy files (edr), run input files (tpr), and the continue points (cpt) at 20 µs are provided. </p> <p>All required input files are also provided to regenerate the run input files: initial structures (gro), index files (ndx), topologies (top and itp), and the common simulation parameter file (mdp). Details of the setup, simulation, and analysis of the systems is available in the preprint:</p> <p>https://doi.org/10.1101/2022.09.30.510141</p>
Martini 2 and Martini 3 simulations of DOPE/DOPC mixtures
<p>Martini simulations of DOPE/DOPC lipid mixtures from 0% to 100% in increments of 10%. Performed with GROMACS.</p>
Supporting data for transmembrane domain self association simulations in "Recalibration of protein interactions in Martini 3"
<p>This repository contains the data of transmembrane helix self-association simulation from "Recalibration of protein interactions in Martini 3". Simulations were run with the Martini 3.0 force field, along with two modified versions of Martini 3.0 in which the well-depth, ε, in the Lennard-Jones potential between all protein and water beads was rescaled by a factor <em>λ</em><sub>PW</sub>, ε in the Lennard-Jones potential between all protein beads was rescaled by a factor <em>λ</em><sub>PP</sub>. The simulation files are kept in one single zip file, which contains trajectories for two protein EphA1 and ErbB1 systems with three versions of force fields. The trajectory files are in xtc format, and are accompanied by a structure in pdb format for system topology and a tpr file to start the simulation. In each version of force field for each protein, name of the files corresponds to that specific umbrella sampling window. Umbrella sampling windows ranges from 0.6 nm to 3.4 nm with a spacing of 0.2 nm. </p>
CG molecular dynamics simulations. Supporting data for "Improving Martini 3 for Disordered and Multidomain Proteins".
<pre>Coarse-grained molecular dynamics simulations with Martini 3 with varying rescaling of protein-water interactions. Supporting data for "Improving Martini 3 for Disordered and Multidomain Proteins".</pre>
FIGURE 3 in Taxonomic notes on Spiraea martini Léveillé (Rosaceae)
FIGURE 3. Leaf variation of Spiraea martini. A. Kunming Botanical Garden, Kunming City, Yunnan; B. West Mountain, Kunming City, Yunnan.
Supporting data for "Recalibration of protein interactions in Martini 3"
<p>Coarse-grained molecular dynamics simulations from "Recalibration of protein interactions in Martini 3". Simulations were run with the Martini 3.0 force field, as well as several modified versions of Martini 3.0 in which the well-depth, ε, in the Lennard-Jones potential between all protein and water beads was rescaled by a factor <em>λ</em><sub>PW</sub>, ε in the Lennard-Jones potential between all protein beads was rescaled by a factor <em>λ</em><sub>PP</sub>, or ε in the Lennard-Jones potential between all protein backbone and water beads was rescaled by a factor <em>λ</em><sub>PW-BB</sub>. The simulation files are organized into one tar file for each rescaling approach. The simulation files are in xtc format, and are accompanied by a structure in gro format that can be used for system topology. There is also a tar file containing the atomistic starting structures used to set up the simulations (in pdb format).</p>
Supporting data for protein membrane simulations in "Recalibration of protein interactions in Martini 3"
<p>Coarse-grained molecular dynamics simulations of protein-membrane systems from "Recalibration of protein interactions in Martini 3". Simulations were run with the Martini 3.0 force field, along with two modified versions of Martini 3.0 in which the well-depth, ε, in the Lennard-Jones potential between all protein and water beads was rescaled by a factor <em>λ</em><sub>PW</sub>, ε in the Lennard-Jones potential between all protein beads was rescaled by a factor <em>λ</em><sub>PP</sub>. The simulation files are organized into one tar file for each rescaling approach. The simulation files are in xtc format, and are accompanied by a structure in gro format for system topology and a tpr file to start the simulation.</p>
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