News
CAVER was recently cited in NATURE paper entitled Growth of complete ammonia oxidizers on guanidine.
CAVER was recently cited in NATURE Communications in the paper entitled Long-range charge transfer mechanism of the III2IV2 mycobacterial supercomplex.
CAVER was recently cited in NATURE Communications in paper entitled Structural insights into drug transport by an aquaglyceroporin.
CAVER was recently cited in NATURE paper entitled Bitter taste receptor activation by cholesterol and an intracellular tastant.
CAVER was recently cited in the article entitled Constitute activation mechanism of a class C GPCR, published in NATURE Structural & Molecular Biology.
CAVER was cited in NATURE Communications paper entitled Molecular mechanism underlying regulation of Arabidopsis CLCa transporter by nucleotides and phospholipids.
CAVER was recently cited by the NATURE publication entitled Structural basis of the binding of DNP and purine nucleotides onto UCP1.
CAVER was recently cited in Nature in paper In situ architecture of the ER–mitochondria encounter structure.
CAVER was recently cited by the paper Symport and antiport mechanisms of human glutamate transporters, published in NATURE Communications.
CAVER was recently cited in paper entitled N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry, published in NATURE Communications.
CAVER was recently cited by a NATURE paper entitled Structural basis for bacterial energy extraction from atmospheric hydrogen.
CAVER was recently cited by an article entitled Cryo-EM structure of human heptameric pannexin 2 channel, published in NATURE Communications.
CAVER was recently cited by NATURE Communications in the article entitled Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes.
CAVER was recently cited by NATURE Communications in the article Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography.
CAVER was cited by the article Conformational changes in the human Cx43/GJA1 gap junction channel visualized using cryo-EM, published in NATURE Communications.
CAVER was recently cited in the publication Structure of the core human NADPH oxidase NOX2, published in NATURE Communications.
CAVER tool was recently cited in the publication O2-tolerant CO dehydrogenase via tunnel redesign for the removal of CO from industrial flue gas, published in Nature Catalysis.
CAVER was cited by the paper The involvement of CYP1A2 in biodegradation of dioxins in pigs, published in PloS ONE.
CAVER was recently cited by the article The coupling mechanism of mammalian mitochondrial complex I, published in Nature Structural & Molecular Biology.
CAVER tool was cited by an article Structural basis of the ligand binding and signaling mechanism of melatonin receptors, published in Nature Communications.
CAVER was recently cited by a publication Structural basis of BAK activation in mitochondrial apoptosis initiation, published in NATURE Communications.
CAVER was recently cited by the publication entitled Structural and functional analysis of the promiscuous AcrB and AdeB efflux pumps suggests different drug binding mechanisms, which was publised in NATURE Communications.
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 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 was recently cited by the NATURE paper entitled Dispatched uses Na+flux to power release of lipid-modified Hedgehog.
CAVER was recently cited in by the paper entitled Crystal structure of a key enzyme for anaerobic ethane activation, published in Science.
CAVER was recently cited in the NATURE Communications article entitled Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity.
CAVER was cited in NATURE Communications in the article Structure-guided insights into heterocyclic ring-cleavage catalysis of the non-heme Fe (II) dioxygenase NicX.
CAVER was recently cited in NATURE Communications in paper Active-site loop variations adjust activity and selectivity of the cumene dioxygenase.
CAVER was recently cited in NATURE Scientific Reports, in article entitled Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists.
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 was cited in NATURE Communications in the paper ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria.
CAVER was recently cited in a NATURE Communications publication entitled Essential role of accessory subunit LYRM6 in the mechanism of mitochondrial complex I.
CAVER was recently cited by the article Cholesterol access in cellular membranes controls Hedgehog signaling, published in Nature Chemical Biology.
CAVER was cited in the NATURE Communications article Antibiotic export by MexB multidrug efflux transporter is allosterically controlled by a MexA-OprM chaperone-like complex.
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 was cited in the NATURE journal in article Structures of human pannexin 1 reveal ion pathways and mechanism of gating.
CAVER was cited in the NATURE journal in paper Femtosecond-to-millisecond structural changes in a light-driven sodium pump.
CAVER was cited in Nucleic Acids Research paper Differences in the path to exit the ribosome across the three domains of life.
CAVER was cited in the NATURE Communications journal in article Structures of the wild-type MexAB–OprM tripartite pump reveal its complex formation and drug efflux mechanism.
CAVER was cited in the Biochemistry jounal in paper Exposing the Interplay Between Enzyme Turnover, Protein Dynamics, and the Membrane Environment in Monoamine Oxidase B.
CAVER was cited in the NATURE paper Serotonin transporter–ibogaine complexes illuminate mechanisms of inhibition and transport.
CAVER was cited in the PLOS Biology paper Structure of the human ClC-1 chloride channel.
CAVER was cited in the NATURE Communications paper Intrinsic enzymatic properties modulate the self-propulsion of micromotors.
CAVER was cited in PNAS in paper The crystal structure of human microsomal triglyceride transfer protein.
CAVER was cited in the JBC paper The ghrelin O-acyltransferase structure reveals a catalytic channel for transmembrane hormone acylation.
CAVER was cited in the Nucleic Acids Research paper Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis.
CAVER was cited in the Nature Structural & Molecular Biology paper Structure of the human lipid exporter ABCB4 in a lipid environment.
CAVER was cited in the Journal of Molecular Biology in paper Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB.
CAVER was cited in the ACS Catalysis journal in article N-Glycosylation and Gaucher Disease Mutation Allosterically Alter Active-Site Dynamics of Acid-β-Glucosidase.
CAVER was cited in the NATURE Communications journal in article Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I.
CAVER was cited in the Current Opinion in Structural Biology article Respiratory complex I — structure, mechanism and evolution.
CAVER was cited in the NATURE Communications journal in article Structural insights into NDH-1 mediated cyclic electron transfer.
CAVER was cited in the Nature Structural & Molecular Biology journal in article Structural and functional characterization of the bestrophin-2 anion channel.
CAVER was cited in the ACS Catalysis journal in paper Structure-Guided Tuning of a Hydroxynitrile Lyase to Accept Rigid Pharmaco Aldehydes.
CAVER was cited in the NATURE journal in article Cryo-EM structure of the human α1β3γ2 GABAA receptor in a lipid bilayer.
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 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 was cited in the NATURE Reviews Chemistry journal in article Extending the application of biocatalysis to meet the challenges of drug development.
CAVER was cited in the NATURE journal in article Cryo-EM reveals two distinct serotonin-bound conformations of full-length 5-HT 3A receptor.
CAVER 3.0 was cited in the PLoS ONE journal in article called How does binding of agonist ligands control intrinsic molecular dynamics in human NMDA receptors?
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 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 was cited in the NATURE journal in article Mechanism of NMDA receptor channel block by MK-801 and memantine.
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 was cited in the ACS Chemical Biology journal in article Functional and Structural Analysis of Phenazine O-Methyltransferase LaPhzM from Lysobacter antibioticus OH13 and One-Pot Enzymatic Synthesis of the Antibiotic Myxin.
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 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 just released. For more information see the download page.
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 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 was cited in the Nature Communications journal in article Lysosomal integral membrane protein-2 as a phospholipid receptor revealed by biophysical and cellular studies.
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 was cited in the ACS Catalysis journal in article Internal Water Dynamics Control the Transglycosylation/Hydrolysis Balance in the Agarase (AgaD) of Zobellia galactanivorans.
CAVER was cited in the Nature Communications journal in article Structure of a MacAB-like efflux pump from Streptococcus pneumoniae.
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 was cited in the NATURE journal in article Electron cryo-microscopy structure of the mechanotransduction channel NOMPC.
CAVER was cited in the NATURE journal in article Structure of a CLC chloride ion channel by cryo-electron microscopy.
CAVER was cited in the NATURE journal in article Crystal structure of the epithelial calcium channel TRPV6.
CAVER was cited in the NATURE journal in article Structural basis of Smoothened regulation by its extracellular domains.
CAVER was cited in the Nature Communications journal in article A CD36 ectodomain mediates insect pheromone detection via a putative tunnelling mechanism.
CAVER was cited in the Journal of Biological Chemistry in the article Control of the Position of Oxygen Delivery in Soybean Lipoxygenase-1 by Amino Acid Side Chains within a Gas Migration Channel.
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 was cited in the Accounts in Chemical Research journal in article Protein Binding Pocket Dynamics.
CAVER was cited in the Science journal in the article The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters.
CAVER was cited in the ACS Catalysis journal in the article Engineering a de Novo Transport Tunnel.
CAVER was cited in the ACS Catalysis journal in the article Evolution of P450 Monooxygenases toward Formation of Transient Channels and Exclusion of Nonproductive Gases.
CAVER was cited in Nucleic Acids Research in the article HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering.
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 was cited in the ACS Catalysis journal in article Evolution of P450 Monooxygenases toward Formation of Transient Channels and Exclusion of Nonproductive Gases.
CAVER was cited in the NATURE journal in article Structure of mammalian respiratory complex I.
CAVER was cited in Nature in the article Structural basis of Smoothened regulation by its extracellular domains.
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 was cited in Nature in the article Crystal structure of the epithelial calcium channel TRPV6.
CAVER was cited in Nature Communications in the article A CD36 ectodomain mediates insect pheromone detection via a putative tunnelling mechanism.
CAVER was cited in the Cell Structure journal in the article A Gating Mechanism of the Serotonin 5-HT3 Receptor.
CAVER was cited in the Journal of Lipid Research in the article Crystal structure of a lipoxygenase from Cyanothece sp. may reveal novel features for substrate acquisition.
CAVER was cited in the Journal of Biological Chemistry in the article Control of the Position of Oxygen Delivery in Soybean Lipoxygenase-1 by Amino Acid Side Chains within a Gas Migration Channel.
CAVER 3.0 was cited in the Science journal in the article Mechanistic insight from the crystal structure of mitochondrial complex I.
CAVER was cited in the Journal of Biological Chemistry journal in article Crystal structure of snake venom acetylcholinesterase in complex with inhibitory antibody fragment Fab410 bound at the peripheral site: evidence for open and closed states of a back door channel.
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 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 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 3.0 was cited in the PLOS Genetics journal in the article Allelic Variation of Cytochrome P450s Drives Resistance to Bednet Insecticides in a Major Malaria Vector.
CAVER was cited in the Chemistry & Biology journal in the article Unraveling the B. pseudomallei Heptokinase WcbL: From Structure to Drug Discovery.
CAVER was cited in the Journal of Biological Chemistry journal in article Structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the LysZ·LysW complex from Thermus thermophilus.
CAVER was cited in the PLoS Computational Biology journal in article Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes.
CAVER was cited in the Journal of Biological Chemistry in article Crystal Structure and Mutational Analysis of Isomalto-dextranase, a Member of Glycoside Hydrolase Family 27.
CAVER was cited in the Journal of Molecular Biology in article A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site.
CAVER was cited in the PLoS ONE journal in article F429 Regulation of Tunnels in Cytochrome P450 2B4: A Top Down Study of Multiple Molecular Dynamics Simulations.
CAVER was cited in the ChemCatChem journal in article Balancing the Stability–Activity Trade-Off by Fine-Tuning Dehalogenase Access Tunnels.
CAVER 3.0 was cited in the Nature journal in article called Structure of the V. cholerae Na+-pumping NADH: quinone oxidoreductase.
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 was cited in the PLoS ONE journal in article Molecular Dynamics of CYP2D6 Polymorphisms in the Absence and Presence of a Mechanism-Based Inactivator Reveals Changes in Local Flexibility and Dominant Substrate Access Channels published on October 6, 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 was cited in the NATURE journal in article X-ray structure of the mouse serotonin 5-HT3 receptor published on August 3, 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 3.0 software was cited in PNAS in the article called Structures of benzylsuccinate synthase elucidate roles of accessory subunits in glycyl radical enzyme activation and activity.
CAVER 3.0 software was cited in PLOS ONE in the article called Ensemble Generation and the Influence of Protein Flexibility on Geometric Tunnel Prediction in Cytochrome P450 Enzymes.
CAVER was cited in the Nature journal in the article Crystal structure of a human GABAA receptor published on June 8, 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 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 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 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.
New article called Computational tools for designing and engineering enzymes was published in the Current Opinion in Chemical Biology journal.
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
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
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.
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
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 was chosen among 5 (from 40) companies to be member of the JIC Innovation Park acceleration program, starting 1.4.2013.
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.
Thank you StarCube, JIC and all who supported us!
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 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 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 the the international life science business plan competition Best of Biotech.
CaverSoft takes part in the StarCube company startup program by South Moravian Innovation Centre.
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 was cited in the PLoS ONE journal in article Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase published on May 4, 2012.
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 was cited in the PLoS ONE journal in article Molecular Dynamics Analysis Reveals Structural Insights into Mechanism of Nicotine N-Demethylation Catalyzed by Tobacco Cytochrome P450 Mono-Oxygenase published on August 16, 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 was cited in the NATURE journal in article Crystal structure of a copper-transporting PIB-type ATPase published on June 29, 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.
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!
