MARTINI statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MARTINI
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Tool usage distribution map

This map represents all the scientific publications referring to MARTINI per scientific context
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Protocols

MARTINI specifications

Information


Unique identifier OMICS_32703
Name MARTINI
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Siewert Marrink

Publication for MARTINI

MARTINI citations

 (117)
library_books

Molecular details of dimerization kinetics reveal negligible populations of transient µ opioid receptor homodimers at physiological concentrations

2018
Sci Rep
PMCID: 5955887
PMID: 29769636
DOI: 10.1038/s41598-018-26070-8

[…] ture was removed and the remaining residues of H8 added so that each structure consisted of sequence residues 65 to 352. The martinize python script was used to coarse grain the structures within the MARTINI v2.2 force field–. A modified version of the elastic network was applied to maintain the receptor tertiary structure,. Specifically, a harmonic force was applied to all backbone (BB) bead pair […]

library_books

Extension of coarse grained UNRES force field to treat carbon nanotubes

2018
J Mol Model
PMCID: 5920012
PMID: 29700628
DOI: 10.1007/s00894-018-3656-1

[…] ESidue (UNRES) force field with a CNT treated as a cylinder with infinite length. UNRES is a coarse-grained force field [–] for protein simulation, which, like other coarse-grained force fields, e.g. Martini [], is constantly being improved and extended to treat not only proteins, but also nucleic acids, sugars, and lipids []. Owing to the simplified representation, UNRES provides an about 1000-fo […]

call_split

Structures of monomeric and oligomeric forms of the Toxoplasma gondii perforin like protein 1

2018
Sci Adv
PMCID: 5943054
PMID: 29750191
DOI: 10.1126/sciadv.aaq0762
call_split See protocol

[…] For coarse-grained simulations, the Martini v2.2 coarse grain force field was used (, ). Lennard-Jones interactions were shifted to zero between 0.9 and 1.1 nm. The electrostatic potential energy was shifted to zero between 0 and 1.1 nm […]

library_books

Closely related, yet unique: Distinct homo and heterodimerization patterns of G protein coupled chemokine receptors and their fine tuning by cholesterol

2018
PLoS Comput Biol
PMCID: 5864085
PMID: 29529028
DOI: 10.1371/journal.pcbi.1006062

[…] ure contained residues from Val37 to Phe320. Finally, both CC chemokine receptor structures were minimized using the CHARMM36 force field [].Subsequently, the protein structures were converted to the Martini2.2 coarse-grained force field [] using martinize []. In order to enforce the secondary and tertiary structure, an elastic RubberBands force network was applied. RubberBands as established in W […]

library_books

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

2018
Front Mol Biosci
PMCID: 5816062
PMID: 29484300
DOI: 10.3389/fmolb.2018.00013

[…] ward large-scale applications and eventually merge it with molecular dynamics simulations. Recently, we adapted VISM to produce solvation free energies for “martinized” proteins (Ricci et al., ). The MARTINI model is a well-established meso-scale force field for modeling large molecular systems, which replaces groups of atoms by interaction centers commonly referred to as “beads,” based on an appr […]

library_books

Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans

2018
PLoS Comput Biol
PMCID: 5814095
PMID: 29401455
DOI: 10.1371/journal.pcbi.1005972

[…] entire mycolactone with respect of the center of mass of the lipid bilayer and along the normal (z) coordinate. For each window, 10 μs long simulations were performed. We should state, however, that MARTINI based simulations lead to an effective speed up of a factor of ~4 [], effectively giving a 40 μs time per window. PMFs were reconstructed using the weighted histogram [] approach and convergen […]


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MARTINI institution(s)
Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for AdVanced Materials, Department of Biophysical Chemistry, University of Groningen, Groningen, The Netherlands; Zernike Institute for Advanced Materials, Department of Applied Physics, University of Groningen, Groningen, The Netherlands; Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
MARTINI funding source(s)
Supported by the Netherlands Organisation for Scientific Research (NWO), an AHFMR Senior Scholar and CIHR New Investigator, and by NSERC.

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