CAVER statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CAVER
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Tool usage distribution map

This map represents all the scientific publications referring to CAVER per scientific context
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Associated diseases

This word cloud represents CAVER usage per disease context
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Popular tool citations

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Protocols

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

Versioning


No version available

Maintainers


  • person_outline Jiri Damborsky
  • person_outline Barbora Kozlikova

Publications for CAVER

CAVER citations

 (126)
library_books

Tracking the route of molecular oxygen in O2 tolerant membrane bound [NiFe] hydrogenase

2018
Proc Natl Acad Sci U S A
PMCID: 5877991
PMID: 29463722
DOI: 10.1073/pnas.1712267115

[…] uce 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 A […]

library_books

Structure Based Virtual Screening Studies to Identify Novel Potential Compounds for GPR142 and Their Relative Dynamic Analysis for Study of Type 2 Diabetes

2018
PMCID: 5817085
PMID: 29492402
DOI: 10.3389/fchem.2018.00023

[…] Figure represents the Trans membrane domains: 160 to 182, TM2 194 to 216, TM3 236 to 258, TM4 278 to 300, TM5 315 to 337, TM6 357 to 379, and TM7 394 to 416. The tunnels were generated using CAVER2.1 program. The tunnel leading to active site had following coordinates; X coordinate at −4.95, Y coordinate at −70.93, and Z coordinate at 66.58. Whereas, bottleneck radius, length, curvature a […]

library_books

Thermal stabilization of the deglycating enzyme Amadoriase I by rational design

2018
Sci Rep
PMCID: 5813194
PMID: 29445091
DOI: 10.1038/s41598-018-19991-x

[…] ues H106 and G150, which are in close proximity to the entrance of the tunnel.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 i […]

library_books

Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841

2018
PLoS One
PMCID: 5806882
PMID: 29425231
DOI: 10.1371/journal.pone.0192736

[…] formational 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 sim […]

call_split

Ligand complex structures of l‐amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 and its conformational change

2018
FEBS Open Bio
PMCID: 5832979
PMID: 29511608
DOI: 10.1002/2211-5463.12387
call_split See protocol

[…] c 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 . […]

library_books

A de novo Ser111Thr variant in aquaporin 4 in a patient with intellectual disability, transient signs of brain ischemia, transient cardiac hypertrophy, and progressive gait disturbance

2018
PMCID: 5793774
PMID: 29437797
DOI: 10.1101/mcs.a002303

[…] The crystal structure was obtained from the RCSB PDB protein data bank (PDB ID: 3GD8; Ho et al. 2009) and subsequently analyzed by CAVER Analyst (). CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures. First, a single channe […]


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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

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