CAVER protocols

CAVER statistics

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CAVER specifications

Information


Unique identifier OMICS_04690
Name CAVER
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Jiri Damborsky <>
  • person_outline Barbora Kozlikova <>

Publications for CAVER

CAVER in pipelines

 (6)
2017
PMCID: 5321766
PMID: 28220900
DOI: 10.1038/ncomms14505

[…] select the appropriated gathering frequency in the pmf curves. bootstrapping of 1,000 samples was used to estimate the standard deviation of the pmf results., tunnel pathways were computed using the caver software. the starting point coordinates were set to centre of the binding pocket of opsin and a2ar. computations were carried out using a shell radius 3 å, shell depth 4 å, a probe radius […]

2017
PMCID: 5591372
PMID: 28928723
DOI: 10.3389/fmicb.2017.01685

[…] i–iv and viii locate at the catalytic pockets (figure and supplementary table s5). therefore, based on the te crystal structure of pksa, 27 clr sites of te domains were predicted by using castp and caver (supplementary table s5). among them, 11 clr sites locate at the lid regions of te domains. it was found that there are nine most conserved clr sites showing the same or similar residues […]

2016
PMCID: 5013575
PMID: 27606012
DOI: 10.1186/s13321-016-0157-z

[…] the visualization of potential energy surfaces and charge densities on protein surfaces. castp [–] detects pockets and voids in protein structures to determine and characterize binding sites, while caver [, ] performs calculations of substrate pathways and entrance tunnels in protein structures, and enables their visualization., in this work, we describe a plugin for pymol which allows carrying […]

2014
PMCID: 4096009
PMID: 25089269
DOI: 10.1155/2014/429486

[…] mesh ewald (pme) option. the 10 ns md trajectories were then analyzed by a series of gromacs protocols, and the presumable pathways for small molecule under dynamic conditions were analyzed by the caver 3.0 program []., the disordered disposition of traf6 protein was predicted by pondr-fit protocol [] with the sequence from swiss-prot (uniprotkb: q9y4k3). the result displayed in indicates […]

2014
PMCID: 4203756
PMID: 24632677
DOI: 10.4161/chan.28136

[…] step of 2 fs was used and bond lengths to hydrogen atoms were kept fixed. the van der waals cutoff was set to 12 å. all figures of the simulation system were produced using vmd 1.9.1., the program caver 3.0 was used to analyze the size and profile of the fenestrations using aligned structural coordinate (.pdb) files corresponding to every 0.1 ns of the md simulation. in this program, the outer […]


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CAVER in publications

 (106)
PMCID: 5877991
PMID: 29463722
DOI: 10.1073/pnas.1712267115

[…] a correlation of o2 occupancy with pressure and incubation time (). to inspect the positions of the o2 molecules with respect to the gas tunnel network, the latter was calculated with the program caver 3.0 (), using the highly conserved residue r530l as the initial starting point (). the program predicts two subunit-crossing tunnels, which merge before reaching the [nife] active site. tunnel […]

PMCID: 5817085
PMID: 29492402
DOI: 10.3389/fchem.2018.00023

[…] adapted in this manuscript is shown as flowchart in figure ., to understand the mechanism of ligand movement and probable binding sites, tunnels were located in the modeled structure of gpr142 using caver2.1 (beneš, ; beneš et al., ). domain predictions were performed using tmbase (hofmann and stoffel, ) and gpcrhmm server (wistrand et al., ). tmbase and gprcrhmm algorithm were based […]

PMCID: 5813194
PMID: 29445091
DOI: 10.1038/s41598-018-19991-x

[…] were performed at 25 °c, as described in the material and methods section., to support this hypothesis, we compared substrate tunnel dimension between the wild type enzyme and the ss07 mutant using caver 3.0.2 software. for the analysis of the geometry of the tunnel, we removed the ions and water molecules that were included in the md runs. in particular, we applied the same protocol developed […]

PMCID: 5806882
PMID: 29425231
DOI: 10.1371/journal.pone.0192736

[…] clustering using the k-means algorithm with k = 20. these states were then assembled into a markovian state model with a lag time of 40 nanoseconds using the pyemma python library []. the caver algorithm [,] was used to identify a number of transiently forming tunnels linking the active sites of each monomer to the surface as well as the central cavity of the tetramer., an additional […]

PMCID: 5832979
PMID: 29511608
DOI: 10.1002/2211-5463.12387

[…] maps yielded an electron density that corresponded to the soaked substrate. figures were prepared using open source pymol (schrödinger, llc, new york, ny, usa), cuemol (http://www.cuemol.org/), and caver 3.0 ., mutations were introduced by pcr using expression plasmid pet15b‐laao/mog as a template and the quikchange kit (stratagene, la jolla, ca, usa) using primers p1 to p10 (table ). […]


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CAVER institution(s)
Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Brno, Czech Republic; Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic; Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Plzen, Czech Republic

CAVER review

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mamapcr

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