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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




No version available


Publication for trj-cavity

trj-cavity citations


Computational Insight Into the Structural Organization of Full Length Toll Like Receptor 4 Dimer in a Model Phospholipid Bilayer

Front Immunol
PMCID: 5857566
PMID: 29593733
DOI: 10.3389/fimmu.2018.00489

[…] tomated 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 (). […]


Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis

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

[…] olecular 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 the alignme […]


Structure and Function of the Su(H) Hairless Repressor Complex, the Major Antagonist of Notch Signaling in Drosophila melanogaster

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

[…] ies 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 []. […]


Identification of an activation site in Bak and mitochondrial Bax triggered by antibodies

Nat Commun
PMCID: 4890306
PMID: 27217060
DOI: 10.1038/ncomms11734

[…] simulations 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. […]


Energetics of Endotoxin Recognition in the Toll Like Receptor 4 Innate Immune Response

Sci Rep
PMCID: 4673606
PMID: 26647780
DOI: 10.1038/srep17997

[…] cutoff of 1.2 nm. Simulation analysis was performed using GROMACS ( 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. […]


Multiple Binding Poses in the Hydrophobic Cavity of Bee Odorant Binding Protein AmelOBP14

J Chem Inf Model
PMCID: 4695918
PMID: 26633245
DOI: 10.1021/acs.jcim.5b00673
call_split See protocol

[…] ters. Water density inside the cavity throughout all snapshots assigned to one cluster was determined using GROMOS++ program iondens with a grid spacing of 0.1 nm.Cavity volumes were calculated using trj_cavity. Structures were visualized using Pymol (; The PyMOL Molecular Graphics System, Version 1.4.1 Schroedinger, LLC). […]

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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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