Wordom protocols

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Wordom specifications

Information


Unique identifier OMICS_17502
Name Wordom
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format XTC, DCD, XYZ
Output format TXT
Operating system Mac OS
Programming languages C
License GNU General Public License version 2.0
Computer skills Medium
Version 0.22
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Francesca Fanelli <>

Additional information


https://sourceforge.net/p/wordom/wikidoc/PyWordom%27s_Guide/

Publication for Wordom

Wordom in pipelines

 (5)
2017
PMCID: 5460117
PMID: 28588190
DOI: 10.1038/s41598-017-01498-6

[…] with other simulation packages, such as amber, charmm and namd after conversion of the md trajectory to the gromacs format (.xtc or.trr file). this can be achieved with several tools such as wordom , the mdanalysis package and the catdcd plugin (http://www.ks.uiuc.edu/development/mdtools/catdcd/). the user can employ the gromacs tool editconf to convert the pdb file of the starting […]

2016
PMCID: 4739762
PMID: 26808983
DOI: 10.7554/eLife.11050.029

[…] (~10,000 atoms) were performed using acemd () in the nvt ensemble at 310 k for the cis and trans configurations and for the r/r, s/r, and s/s stereoisomers. trajectories were analyzed using vmd and wordom (), and molecular snapshots were rendered using pymol (schrödinger, llc). profiles of the tm pore radius along the axis were calculated using the program hole () for backbone atoms […]

2016
PMCID: 4892583
PMID: 27258022
DOI: 10.1371/journal.pone.0157162

[…] into one final pseudo-trajectory. similarly, an ensemble of all structures from nm-displacements into one pseudo-trajectory was conducted. the cross-correlation calculations were performed in the wordom software []., the occurrence of specific interactions in the impα-nplnls interface was evaluated. the determination of salt bridges and hydrogen bonds were performed using the vmd software []. […]

2015
PMCID: 4569070
PMID: 26366880
DOI: 10.1371/journal.pcbi.1004346

[…] by comparing to unconstrained simulations., to identify the collective motions of the whole fg molecule and of its subdomains we performed several principal component analyses (pca) [] using wordom [] and gromacs utilities []. dyndom [] was used to identify rigid domains and hinges of motion. the overlap between spaces spanned by the dominant pca modes of different simulations was used […]

2014
PMCID: 4066822
PMID: 24694723
DOI: 10.1038/ncomms4590

[…] were removed and an equilibration run was performed. md simulations were performed for 25 ns with the time step of 2 fs. the configurations and velocities were stored every 2 ps. the programs vmd, wordom, dssp, apbs, were used for assessment of protein structure stability, rmsd and visualization., o.d thanks prof. luis g. cuello for enlightening discussion throughout the course of this work. […]


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Wordom in publications

 (37)
PMCID: 5958240
PMID: 29660325
DOI: 10.1016/j.jmb.2018.04.006

[…] to analysis to avoid starting structure bias. for the shorter coiled coil sections, simulations ran for 275 ns, with frames recorded every 500 steps., simulation trajectories were analyzed using wordom . the helicity of both chains was calculated using backbone dihedral angles and the method previously described . rmsd values for all cα atoms were calculated with respect to the initial […]

PMCID: 5690683
PMID: 29108014
DOI: 10.1371/journal.pcbi.1005826

[…] obtained by combining the last 100 ns of all the apo and om-bound trajectories., the correlation networks were generated by calculating the dynamical cross-correlation (dcc) matrices with wordom [] using cα atoms coordinates of snapshots extracted from the production trajectory every 100 ps. multiple matrices were first generated by calculating time averages over 5 ns. averaging […]

PMCID: 5673239
PMID: 29069080
DOI: 10.1371/journal.pcbi.1005784

[…] ion pore, its ion and water permeability, and the configuration of the orthosteric neurotransmitter site and the allosteric transmembrane site. all observables have been implemented in the program wordom (version 0.23-rc1 available at https://sourceforge.net/p/wordom/codehg) to allow for efficient analysis of long md trajectories., the global twisting (τ) was evaluated per subunit and defined […]

PMCID: 5542433
PMID: 28771551
DOI: 10.1371/journal.pone.0182387

[…] k, 100 ns for cathepsin k/substrate and cathepsin k/c4s complexes, and for cathepsins l, v, s and f, 125 ns for the cathepsin k/nsc94914 complex and 240 ns for the cathepsin k/nsc13345 complex., the wordom program [] was used to calculate average structures (average md conformers)from the trajectories, to calculate rmsf and per-frame distances between designated atom pairs, as described […]

PMCID: 5501500
PMID: 28695211
DOI: 10.1126/sciadv.1700479

[…] obtained were then analyzed, and the 10% of the structures that had the lowest energy were selected. we performed a clustering analysis on these structures using the algorithm implemented in wordom and gromacs (, )., we calculated the distribution for the pairwise rmsd values between the cα atoms of the selected structures and defined the highest peak of the obtained distribution […]


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Wordom institution(s)
Department of Life Sciences, Modena, Italy; Dulbecco Telethon Institute (DTI), Modena, Italy
Wordom funding source(s)
This study was supported by an Airc-Italy grant [IG10740] and a Telethon-Italy grant [GGP11210/S00068TELC].

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