trj-cavity statistics

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trj-cavity specifications

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Unique identifier OMICS_13828
Name trj-cavity
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format PDB
Output data Provides a structure file of the cavity found when working with a single structure, or the topology file to visualize the trajectory of the cavity when working with trajectories; a file with the volume of the cavity for each trajectory frame; a trajectory of the cavity found throughout the trajectory provided.
Output format PDB
Operating system Unix/Linux
Computer skills Advanced
Version 2.1
Stability Stable
Maintained Yes

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Publication for trj-cavity

trj-cavity in publications

 (8)
PMCID: 5857566
PMID: 29593733
DOI: 10.3389/fimmu.2018.00489

[…] topology builder server () which uses a hybrid quantum mechanics/molecular mechanics method for assigning partial charges to atoms. the volume of the md2 hydrophobic cavity was computed using trj_cavity_v2.0 program ()., two separate md simulations were performed for the isolated tlr4-tir dimers in two different dimeric orientations, as reported in the literature (, , , ). the models […]

PMCID: 5620967
PMID: 28979936
DOI: 10.1021/acscentsci.7b00211

[…] surfaces and probes (e.g., hole, surfnet). other algorithms analyze ensembles of structures, but usually require a preliminary structural alignment (e.g., mdpocket, pocketanalizerpca, epock, trj_cavity, and trapp). in this case, the resulting information may depend on the specific reference structure used for the alignment. atom-based algorithms (e.g., provar and eposbp) avoid […]

PMCID: 4942083
PMID: 27404588
DOI: 10.1371/journal.pbio.1002509

[…] was performed with the ambertools 1.5, gromacs [] and rstudio packages. cavity analysis of the most representative structures of the principal clusters of the su(h) trajectory was performed using trj_cavity []., the yeast two- and three-hybrid experiments were performed in triplicate as described previously [,]. peg-mam corresponds to d. melanogaster mastermind, comprising codons 118 to 194. […]

PMCID: 4890306
PMID: 27217060
DOI: 10.1038/ncomms11734

[…] were performed on both the unbound bak and the final bak-7d10 complex obtained from the rdock analysis; these simulations were each run for 100 ns. cavity analysis was performed using the trj_cavity tool., the authors declare that all data supporting the findings of this study are available within the article and its files., how to cite this article: iyer, s. et al. identification […]

PMCID: 4673606
PMID: 26647780
DOI: 10.1038/srep17997

[…] of 1.2 nm. simulation analysis was performed using gromacs (http://www.gromacs.org) and vmd. characterization of the time-dependent shape of the maximal md-2 binding cavity was performed using trj_cavity using default options. unless otherwise stated, averages/standard deviations were calculated over the last 5 ns of each pmf., during us, a harmonic potential with force constant of 1000 kj […]


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trj-cavity institution(s)
Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK; Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA; Bioinformatics Institute (A*STAR), Singapore; Department of Biological Sciences, National University of Singapore, Singapore

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