CGMD statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

CGMD specifications

Information


Unique identifier OMICS_11843
Name CGMD
Alternative name Cancer Gene Marker Database
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

Taxon


  • Primates
    • Homo sapiens

Maintainer


This tool is not available anymore.

Publication for Cancer Gene Marker Database

CGMD citations

 (11)
library_books

Lipid bodies containing oxidatively truncated lipids block antigen cross presentation by dendritic cells in cancer

2017
Nat Commun
PMCID: 5730553
PMID: 29242535
DOI: 10.1038/s41467-017-02186-9

[…] in 10% and in 20% of the TAG molecules. Two simulations for each system, total of six simulations, were run and analyzed to assess the number of TAG molecules that were able to leave the core region. CGMD simulations were performed using the GROMACS v. 4.5.4 MD package []. The system was minimized for 20 ps, before 0.2 ns NPT ensemble equilibration followed by a 0.2 ns NVT ensemble equilibration. […]

library_books

The Effect of Tethers on Artificial Cell Membranes: A Coarse Grained Molecular Dynamics Study

2016
PLoS One
PMCID: 5063460
PMID: 27736860
DOI: 10.1371/journal.pone.0162790

[…] The coarse-grained molecular dynamics simulations were performed using GROMACS [] version 4.6.2 (double precision) with the MARTINI force field [, ]. Unless otherwise stated, the CGMD simulation parameters are provided in [, ]. The interaction of the CGMD beads are defined by the Lennard-Jones (LJ) potential, and harmonic potentials are utilized for bond and angle interactions […]

call_split

Coarse grained molecular dynamics studies of the translocation mechanism of polyarginines across asymmetric membrane under tension

2015
Sci Rep
PMCID: 4522684
PMID: 26235300
DOI: 10.1038/srep12808
call_split See protocol

[…] CGMD simulation is a powerful tool for studying CPP–biomembrane interactions that presents a larger system and longer simulation time than traditional all-atom simulations. As a typical coarse-grained […]

library_books

MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes

2015
PMCID: 4509712
PMID: 26073602
DOI: 10.1016/j.str.2015.05.006

[…] tomic resolution model of their membrane environment. The whole process is automated, from the detection of membrane protein structures in the PDB upon its release, through preparation and running of CGMD simulations to their subsequent analysis, conversion to ATMD models, and deposition in the freely and publicly accessible MemProtMD database (http://sbcb.bioch.ox.ac.uk/memprotmd; ). The latter c […]

call_split

A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa

2014
PMCID: 4118822
PMID: 25084326
DOI: 10.1107/S1399004714001850
call_split See protocol

[…] ere hampered by the lack of a membrane, leading to conformations that would not be possible in vivo. Therefore, to investigate potential inter­actions of AlgK with AlgE (with the T8 loop disordered), CGMD simulations were performed. Five independent starting configurations were generated in the following manner. A new set of AlgE protein CG parameters was generated using the final frame of the ato […]

library_books

A Multiscale Approach to Modelling Drug Metabolism by Membrane Bound Cytochrome P450 Enzymes

2014
PLoS Comput Biol
PMCID: 4102395
PMID: 25033460
DOI: 10.1371/journal.pcbi.1003714

[…] ed in a cubic box of water with the length of the longest side from the initial calculations (see for box dimensions).Convergence is a vital issue in MD simulations, which is why several independent CGMD simulations and 3 repeats of each 50 ns atomistic simulation were performed. This is generally regarded as better than running a single longer simulation. It is difficult to prove convergence, b […]

Citations

Looking to check out a full list of citations?

CGMD institution(s)
Division of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati- Andhra Pradesh, India; Department of Biotechnology, Vikrama Simhapuri University, Andhra Pradesh, India; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal

CGMD reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review CGMD