trj-cavity protocols

trj-cavity computational protocol

trj-cavity specifications


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 pipeline

PMCID: 4673606
PMID: 26647780
DOI: 10.1038/srep17997

[…] toff of 1.2 nm. simulation analysis was performed using gromacs ( and vmd68. characterization of the time-dependent shape of the maximal md-2 binding cavity was performed using trj_cavity using default options69. 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 k […]

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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