News

CAVER cited in NATURE Communications
November 16, 2021

CAVER was recently cited by the paper Structure of Escherichia coli cytochrome bd-II type oxidase with bound aurachin D, published in NATURE Communications.

CAVER cited in NATURE Communications
November 16, 2021

CAVER was cited by the paper entitled Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition, published in NATURE Communications.

CAVER cited in NATURE
November 2, 2021

CAVER was recently cited by the NATURE paper entitled Dispatched uses Na+flux to power release of lipid-modified Hedgehog.

CAVER cited in Science
July 13, 2021

CAVER was recently cited in by the paper entitled Crystal structure of a key enzyme for anaerobic ethane activation, published in Science.

CAVER cited in NATURE Communications
May 8, 2021
CAVER cited in NATURE Communications
March 5, 2021
CAVER cited in NATURE Communications
February 23, 2021

CAVER was recently cited in NATURE Communications in paper Active-site loop variations adjust activity and selectivity of the cumene dioxygenase.

CAVER cited in NATURE Scientific Reports
February 18, 2021
CAVER cited in NATURE Communications
January 12, 2021

CAVER was cited in NATURE Communications in the paper entitled Structures of human dual oxidase 1 complex in low-calcium and high-calcium states.

CAVER cited in NATURE Communications
January 11, 2021

CAVER was cited in NATURE Communications in the paper ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria.

CAVER cited in NATURE Communications
December 1, 2020

CAVER was recently cited in a NATURE Communications publication entitled Essential role of accessory subunit LYRM6 in the mechanism of mitochondrial complex I.

CAVER cited in Nature Chemical Biology
November 22, 2020

CAVER was recently cited by the article Cholesterol access in cellular membranes controls Hedgehog signaling, published in Nature Chemical Biology.

CAVER cited in NATURE Communications
October 5, 2020
CAVER cited in NATURE Communications
September 26, 2020

CAVER was recently cited by the article Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico, published in NATURE Communications.

CAVER cited in NATURE
June 8, 2020

CAVER was cited in the NATURE journal in article Structures of human pannexin 1 reveal ion pathways and mechanism of gating.

CAVER cited in NATURE
May 23, 2020

CAVER was cited in the NATURE journal in paper Femtosecond-to-millisecond structural changes in a light-driven sodium pump.

CAVER cited in Nucleic Acids Research
May 13, 2020
CAVER cited in NATURE Communications
May 13, 2020
CAVER cited in Biochemistry
May 13, 2020
CAVER cited in NATURE
May 13, 2020
CAVER cited in PLOS Biology
May 13, 2020

CAVER was cited in the PLOS Biology paper Structure of the human ClC-1 chloride channel.

CAVER cited in NATURE Communications
May 13, 2020

CAVER was cited in the NATURE Communications paper Intrinsic enzymatic properties modulate the self-propulsion of micromotors.

CAVER cited in PNAS
May 13, 2020
CAVER cited in JBC
May 13, 2020
CAVER cited in Nucleic Acids Research
May 13, 2020
CAVER cited in Nature Structural & Molecular Biology
May 13, 2020

CAVER was cited in the Nature Structural & Molecular Biology paper Structure of the human lipid exporter ABCB4 in a lipid environment.

CAVER cited in JMB
May 13, 2020

CAVER was cited in the Journal of Molecular Biology in paper Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB.

CAVER cited in ACS Catalysis
May 13, 2020
CAVER cited in NATURE Communications
May 13, 2020

CAVER was cited in the NATURE Communications journal in article Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I.

CAVER cited in Current Opinion in Structural Biology
May 13, 2020

CAVER was cited in the Current Opinion in Structural Biology article Respiratory complex I — structure, mechanism and evolution.

CAVER cited in NATURE Communications
May 13, 2020

CAVER was cited in the NATURE Communications journal in article Structural insights into NDH-1 mediated cyclic electron transfer.

CAVER cited in Nature Structural & Molecular Biology
May 13, 2020

CAVER was cited in the Nature Structural & Molecular Biology journal in article Structural and functional characterization of the bestrophin-2 anion channel.

CAVER cited in ACS Catalysis
May 13, 2020

CAVER was cited in the ACS Catalysis journal in paper Structure-Guided Tuning of a Hydroxynitrile Lyase to Accept Rigid Pharmaco Aldehydes.

CAVER cited in NATURE
January 8, 2019

CAVER was cited in the NATURE journal in article Cryo-EM structure of the human α1β3γ2 GABAA receptor in a lipid bilayer.

CAVER cited in NATURE Communications
January 8, 2019

CAVER was cited in the NATURE Communications journal in article Cryo-EM structures of KdpFABC suggest a K+ transport mechanism via two inter-subunit half-channels.

CAVER cited in PNAS
January 8, 2019

CAVER was cited in the Proceedings of the National Academy of Sciences journal in article Noncanonical role for the binding protein in substrate uptake by the MetNI methionine ATP Binding Cassette (ABC) transporter.

CAVER cited in NATURE Reviews Chemistry
January 8, 2019

CAVER was cited in the NATURE Reviews Chemistry journal in article Extending the application of biocatalysis to meet the challenges of drug development.

CAVER cited in NATURE
January 8, 2019
CAVER in PLOS ONE
August 10, 2018
CAVER in PLOS ONE
July 26, 2018

CAVER 3.0 was cited in the PLoS ONE journal in article called Insights into molecular mechanisms of drug metabolism dysfunction of human CYP2C9*30.

CAVER in PLOS ONE
July 26, 2018

CAVER 3.0 and CAVER Analyst 1.0 were cited in the PLoS ONE journal in article called Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access.

CAVER cited in NATURE
July 26, 2018

CAVER was cited in the NATURE journal in article Mechanism of NMDA receptor channel block by MK-801 and memantine.

CAVER cited in NATURE Structural & Molecular Biology
July 26, 2018

CAVER was cited in the NATURE Structural & Molecular Biology journal in article Cryo-EM structures of complex I from mouse heart mitochondria in two biochemically defined states.

CAVER cited in ACS Chemical Biology
July 26, 2018
CAVER cited in Current Opinion in Structural Biology
July 26, 2018

CAVER was cited in the Current Opinion in Structural Biology journal in article Protein super-secondary structure and quaternary structure topology: theoretical description and application.

CAVER cited in PNAS
February 26, 2018

CAVER was cited in the Proceedings of the National Academy of Sciences journal in article Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase.

Caver Analyst 2.0 (Beta) has been released.
February 14, 2018

Caver Analyst 2.0 (Beta) has been just released. For more information see the download page.

CAVER cited in PNAS
February 13, 2018

CAVER was cited in the Proceedings of the National Academy of Sciences journal in article Capturing LTA4 hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB4 synthesis.

CAVER cited in Current Opinion in Chemical Biology
February 13, 2018

CAVER was cited in the Current Opinion in Chemical Biology journal in article Computational tools for enzyme improvement: why everyone can – and should – use them.

CAVER cited in Nature Communications
February 13, 2018
CAVER cited in PNAS
February 13, 2018

CAVER was cited in the Proceedings of the National Academy of Sciences journal in article Structure of a lipid A phosphoethanolamine transferase suggests how conformational changes govern substrate binding.

CAVER cited in ACS Catalysis
February 13, 2018
CAVER cited in Nature Communications
February 13, 2018

CAVER was cited in the Nature Communications journal in article Structure of a MacAB-like efflux pump from Streptococcus pneumoniae.

CAVER cited in PNAS
August 7, 2017

CAVER was cited in the Proceedings of the National Academy of Sciences journal in article Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits.

CAVER cited in Nature
July 11, 2017

CAVER was cited in the NATURE journal in article Electron cryo-microscopy structure of the mechanotransduction channel NOMPC.

CAVER cited in Nature
January 18, 2017

CAVER was cited in the NATURE journal in article Structure of a CLC chloride ion channel by cryo-electron microscopy.

CAVER cited in Nature
January 18, 2017

CAVER was cited in the NATURE journal in article Crystal structure of the epithelial calcium channel TRPV6.

CAVER cited in Nature
January 18, 2017

CAVER was cited in the NATURE journal in article Structural basis of Smoothened regulation by its extracellular domains.

CAVER cited in Nature Communications
January 18, 2017

CAVER was cited in the Nature Communications journal in article A CD36 ectodomain mediates insect pheromone detection via a putative tunnelling mechanism.

CAVER cited in JBC
January 18, 2017
CAVER cited in JBC
January 18, 2017

CAVER was cited in the Journal of Biological Chemistry in the article Structure of the Catalytic Domain of the Class I Polyhydroxybutyrate Synthase from Cupriavidus necator.

CAVER cited in Accounts in Chemical Research
January 18, 2017

CAVER was cited in the Accounts in Chemical Research journal in article Protein Binding Pocket Dynamics.

CAVER cited in Science
January 18, 2017
CAVER cited in ACS Catalysis
January 18, 2017

CAVER was cited in the ACS Catalysis journal in the article Engineering a de Novo Transport Tunnel.

CAVER cited in ACS Catalysis
January 18, 2017
CAVER cited in NAR
January 18, 2017
CAVER cited in JBC
October 18, 2016

CAVER was cited in the Journal of Biological Chemistry in the article Structure of the Catalytic Domain of the Class I Polyhydroxybutyrate Synthase from Cupriavidus necator.

CAVER cited in ACS Catalysis
October 9, 2016
CAVER cited in NATURE
August 16, 2016

CAVER was cited in the NATURE journal in article Structure of mammalian respiratory complex I.

CAVER cited in Nature
August 10, 2016
CAVER cited in JBC
August 10, 2016

CAVER was cited in the Journal of Biological Chemistry in the article Structural plasticity of cholesteryl ester transfer protein assists its lipid transfer activity.

CAVER cited in Nature
June 20, 2016

CAVER was cited in Nature in the article Crystal structure of the epithelial calcium channel TRPV6.

CAVER cited in Nature Communications
June 20, 2016
CAVER cited in Structure
April 26, 2016

CAVER was cited in the Cell Structure journal in the article A Gating Mechanism of the Serotonin 5-HT3 Receptor.

CAVER cited in JLR
April 26, 2016
CAVER cited in JBC
April 26, 2016
CAVER cited in Science
April 23, 2016

CAVER 3.0 was cited in the Science journal in the article Mechanistic insight from the crystal structure of mitochondrial complex I.

CAVER cited in PNAS
April 23, 2016

CAVER was cited in the Proceedings of the National Academy of Sciences journal in article Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure.

CAVER cited in JBC
April 23, 2016

CAVER was cited in the Journal of Biological Chemistry journal in article Coq6 Is Responsible for the C4-deamination Reaction in Coenzyme Q Biosynthesis in Saccharomyces cerevisiae.

CAVER cited in PLOS Pathogens
April 23, 2016

CAVER 3.0 was cited in the PLOS Pathogens journal in the article A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT.

CAVER cited in PLOS Genetics
April 23, 2016
CAVER cited in Chemistry & Biology
April 23, 2016

CAVER was cited in the Chemistry & Biology journal in the article Unraveling the B. pseudomallei Heptokinase WcbL: From Structure to Drug Discovery.

CAVER cited in JBC
April 23, 2016
CAVER cited in PLOS Computational Biology
April 23, 2016
CAVER cited in JBC
April 23, 2016
CAVER cited in JMB
April 23, 2016

CAVER was cited in the Journal of Molecular Biology in article A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site.

CAVER cited in PLOS ONE
April 23, 2016
CAVER cited in ChemCatChem
April 23, 2016
CAVER cited in Nature
December 16, 2014

CAVER 3.0 was cited in the Nature journal in article called Structure of the V. cholerae Na+-pumping NADH: quinone oxidoreductase.

CAVER in PNAS
October 14, 2014

CAVER was cited in the Proceedings of the National Academy of Sciences journal in article Structural basis of the regulatory mechanism of the plant CIPK family of protein kinases controlling ion homeostasis and abiotic stress approved on September 15, 2014.

CAVER Cited in PLoS ONE
October 14, 2014
CAVER Cited in NATURE
August 23, 2014

CAVER was cited in the NATURE journal in article Structure and mechanism of Zn2+-transporting P-type ATPases published on August 17, 2014.

CAVER Cited in NATURE
August 8, 2014

CAVER was cited in the NATURE journal in article X-ray structure of the mouse serotonin 5-HT3 receptor published on August 3, 2014.

CAVER Cited in PLoS Computational Biology
July 24, 2014

CAVER was cited in the PLoS Computational Biology journal in article A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes published on July 17, 2014.

CAVER Cited in PNAS
July 5, 2014
CAVER Cited in PLOS ONE
July 1, 2014
CAVER Cited in NATURE
June 23, 2014

CAVER was cited in the Nature journal in the article Crystal structure of a human GABAA receptor published on June 8, 2014.

CAVER Analyst published in Bioinfiormatics
June 23, 2014

We announce the publication of the article CAVER Analyst 1.0: Graphic tool for interactive visualization and analysis of tunnels and channels in protein structures in the Bioinformatics Journal! Authors are Barbora Kozlíková, Eva Šebestová, Vilém Šustr, Jan Brezovský, Ondřej Strnad, Lukáš Daniel, David Bednář, Antonín Pavelka, Martin Maňák, Martin Bezděka, Petr Beneš, Matúš Kotry, Artur Wiktor Gora, Jiří Damborský and Jiří Sochor. Publication was accepted on May 22, 2014.

CaverSoft at 11th World Congress on Industrial Biotechnology, Philadelphia, USA (May 12th - 15th)
May 9, 2014

CaverSoft will be attending and presenting at 11th World Congress on Industrial Biotechnology in Philadelphia, Pennsylvania, from May 12 to May 15.

Come and speak with CaverSoft CEO Ondrej Valina and learn more about our product CAVER Analyst 1.0.

Ondrej will be presenting the poster "CAVER Analyst - Engineering of Enzymes by Modification of Access Tunnels" and demoing CAVER Analyst during the poster session. You can also bring your computer and try CAVER Analyst immediately with the assistance.

CAVER cited in PNAS
March 10, 2014

CAVER was cited in the Proceedings of the National Academy of Sciences journal in article Binding of Pro-Gly-Pro at the active site of leukotriene A4 hydrolase/aminopeptidase and development of an epoxide hydrolase selective inhibitor published on February 4, 2014.

New US Patent issued: Method of thermostabilization of a protein and/or stabilization towards organic solvents
January 27, 2014

New US pattent number 8,580,932 was issued on December 12, 2013:

Thermostabilization of a protein where the protein contains access routes and wherein at least one amino acid in the bottleneck of the access route is mutated, includes identifying the amino acids of the bottleneck and the amino acids control exchange of the solvent between a buried protein core and surrounding environment and/or in the packing of the amino acids inside the access route. Modification of the amino acids are determined so that the packing of the amino acids inside the tunnel is improved and the access route prevents access of undesired solvent molecules to the protein core, while allowing passage of the compounds necessary at the protein core to enable the protein to perform its biological function.

Click here to view detailed information.

New publication: Computational tools for designing and engineering enzymes
January 3, 2014
CAVER Analyst 1.0 launched
December 20, 2013

Today we proudly announce the release of CAVER Analyst 1.0 - a novel analytic tool for interactive analysis and visualization of tunnels and channels in protein structures developed in cooperation between CaverSoft, Ltd., Masaryk University and University of West Bohemia.

You can download the application in our download section.

Important new features:

  • Computation of pathways using CAVER 3.01 algorithm
  • Visualization of identified access pathways
  • Display of detailed pathway statistics
  • Identification of residues lining given pathway and its bottleneck
  • Computation of pathway profiles
  • Analysis of pathway dynamics by animation and heat plots
  • Detection and visualization of cavities and molecular surfaces
CAVER Webinar for Harvard Medical School - video record
August 7, 2013

Dr. Jan Brezovsky presented a webinar on the CAVER software for the supercomputing center SBGRid of Harvard Medical School called

CAVER 3.0: Analysis of Tunnels in Static and Dynamic Protein Structures

You can watch the whole video record here.

CaverSoft at BIOTRANS 2013, Manchester, UK (July 21th - 25th)
July 15, 2013

CaverSoft will be attending and presenting at BIOTRANS 2013 in Manchester, United Kingdom, from July 21th-25th.

Come speak with CaverSoft scientists and learn about our latest product CAVER Analyst 1.0 BETA.

CEO Ondrej Valina will be presenting the poster "CAVER Analyst - Engineering of Enzymes by Modification of Access Tunnels" and demoing CAVER Analyst during the poster sessions.

In addition, CAVER Analyst developers Barbora Kozlikova and Vilem Sustr will be available to answer questions during the demo session. You can also bring your computer and try CAVER Analyst 1.0 BETA immediately with our assistance.

BIOTRANS 2013

Jan Brezovsky - Webinar for Harvard Medical School
June 5, 2013

Dr. Jan Brezovsky will be presenting a webinar on the CAVER software for the supercomputing center SBGRid of Harvard Medical School called

CAVER 3.0: Analysis of Tunnels in Static and Dynamic Protein Structures

Thursday, June 13th at 11:00am EST

Detailed information at SBGRid Consortium webpage.

New Publication in Chemical Reviews
May 20, 2013

We announce the publication of the review Gates of Enzymes in the Chemical Reviews, authors are Artur Gora, Jan Brezovsky and Jiri Damborsky. Published on April 25, 2013.

CaverSoft joined JIC Innovation Park
April 22, 2013

CaverSoft was chosen among 5 (from 40) companies to be member of the JIC Innovation Park acceleration program, starting 1.4.2013.

JIC Innovation Park

CaverSoft awarded first prize in StarCube
December 8, 2012

CaverSoft took part in the autumn 2012 run of StarCube startup acceleration program organized by the South Moravian Innovation Centre (JIC) in Brno, Czech Republic. At the closing event of StarCube - the StarCube Show, the team was awarded with the prize of the audience, the prize of ihned.cz and the first prize in the StarCube program decided by independent jury of local and foreign enterpreneurs.

CaverSoft at StarCube

Thank you StarCube, JIC and all who supported us!

CAVER 3.0 published in PLoS Computational Biology
November 9, 2012

CAVER 3.0 was recently published in the PLoS Computational Biology Journal, article called CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures.

CaverSoft in Silicon Valley
November 8, 2012

CaverSoft won virtual office in the Silicon Valley in the Silicon Valley Startup Camp competition organized by US Market Access Center and Czech ICT Alliance. See the whole official press release at www.czechict.cz.

CaverSoft placed top ten in Best of Biotech 2012
October 20, 2012

CaverSoft placed among top ten best projects in the Best of Biotech 2012 international business plan competition in Vienna. Read more at www.bestofbiotech.at.

CaverSoft takes part in Best of Biotech
September 24, 2012

CaverSoft takes part in the the international life science business plan competition Best of Biotech.

CaverSoft takes part in StarCube
September 19, 2012

CaverSoft takes part in the StarCube company startup program by South Moravian Innovation Centre.

CAVER Cited in JBC
June 28, 2012

CAVER was cited in the Journal of Biological Chemistry journal in article A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase LinB. published on June 28, 2012.

CAVER Cited in PLoS ONE
May 4, 2012
CAVER Cited in PLoS ONE
September 7, 2011

CAVER was cited in the PLoS ONE journal in article Molecular Basis of Ligand Dissociation in β-Adrenergic Receptors published on September 7, 2011.

CAVER Cited in PLoS ONE
August 16, 2011
CAVER Cited in PNAS
August 9, 2011

CAVER was cited in the Proceedings of the National Academy of Sciences journal in article The pivotal twin histidines and aromatic triad of the Escherichia coli ammonium channel AmtB can be replaced published on August 9, 2011.

CAVER Cited in NATURE
July 29, 2011

CAVER was cited in the NATURE journal in article Crystal structure of a copper-transporting PIB-type ATPase published on June 29, 2011.

CAVER 2.1 PyMOL Plugin Released
January 20, 2011

We are proud to announce the release of the new version of CAVER 2 PyMOL plugin. The released version 2.1 offers new features like improved Windows installer or better control over input model via graphical user interface. The new version can be accessed in the download section.

New Website Launched
January 14, 2011

We are pleased to oficially announce an upgrade of CAVER website. The website will grow further in near future for the users to get all the support they could possibly need and for us to obtain greatly valued user feedback.

If you have any trouble or suggestions when using our new webpage, please let us know and we will try to fix the issue as soon as possible. Thank you!

CAVER in Nature Methods
December 9, 2010
CAVER was covered by the recent review on visualization tools providing insights to important biological questions published in Nature Methods.
CAVER in PNAS
December 9, 2010
CAVER enabled prediction of possible cavities for ligand binding of negative regulator of transcription TcaR published in the Proceedings of the National Academy of Sciences of the United States of America.


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1219 citations
6071 registered users
111469x CAVER downloaded

news

CAVER was recently cited by the paper Structure of Escherichia coli cytochrome bd-II type oxidase...

Read more

CAVER was cited by the paper entitled Structural dynamics in the water and proton channels of...

Read more

November 2, 2021

CAVER was recently cited by the NATURE paper entitled Dispatched uses Na+flux to power release of...

Read more


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