Blau, Christian

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[["dc.bibliographiccitation.firstpage","4093-4099"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Journal of Chemical Information and Modeling"],["dc.bibliographiccitation.lastpage","4099"],["dc.bibliographiccitation.volume","59"],["dc.contributor.author","Abraham, Mark"],["dc.contributor.author","Apostolov, Rossen"],["dc.contributor.author","Barnoud, Jonathan"],["dc.contributor.author","Bauer, Paul"],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Bonvin, Alexandre M. J. J."],["dc.contributor.author","Chavent, Matthieu"],["dc.contributor.author","Chodera, John"],["dc.contributor.author","Čondić-Jurkić, Karmen"],["dc.contributor.author","Delemotte, Lucie"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Howard, Rebecca J."],["dc.contributor.author","Jordan, E. Joseph"],["dc.contributor.author","Lindahl, Erik"],["dc.contributor.author","Ollila, O. H. Samuli"],["dc.contributor.author","Selent, Jana"],["dc.contributor.author","Smith, Daniel G. A."],["dc.contributor.author","Stansfeld, Phillip J."],["dc.contributor.author","Tiemann, Johanna K. S."],["dc.contributor.author","Trellet, Mikael"],["dc.contributor.author","Wood, Christopher"],["dc.contributor.author","Zhmurov, Artem"],["dc.date.accessioned","2020-04-02T14:32:48Z"],["dc.date.available","2020-04-02T14:32:48Z"],["dc.date.issued","2019-10-28"],["dc.description.abstract","Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations has become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 ( https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/ ). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way toward more open, interoperable, and reproducible outputs coming from research studies using MD simulations."],["dc.identifier.doi","10.1021/acs.jcim.9b00665"],["dc.identifier.pmid","31525920"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/63555"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/199"],["dc.language.iso","en"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.eissn","1549-960X"],["dc.relation.issn","1549-9596"],["dc.relation.issn","1549-960X"],["dc.relation.workinggroup","RG Grubmüller"],["dc.title","Sharing Data from Molecular Simulations"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","663a"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","104"],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Schröder, Gunnar F."],["dc.contributor.author","Fischer, Niels"],["dc.contributor.author","Stark, Holger"],["dc.contributor.author","Rodnina, Marina V."],["dc.contributor.author","Vaiana, Andrea C."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:57:55Z"],["dc.date.available","2021-03-05T08:57:55Z"],["dc.date.issued","2013"],["dc.identifier.doi","10.1016/j.bpj.2012.11.3662"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79932"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Rate Estimates from Sampling Sparse Transitions: TRNA Motion Limits Transitions between Ribosomal Translocation Intermediates"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","491a"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","106"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Vaiana, Andrea C."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:57:57Z"],["dc.date.available","2021-03-05T08:57:57Z"],["dc.date.issued","2014"],["dc.identifier.doi","10.1016/j.bpj.2013.11.2748"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79943"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Concerted Interactions between Ribosomal Subunits Allow for Large-Scale Rotations"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","6747"],["dc.bibliographiccitation.issue","14"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","6760"],["dc.bibliographiccitation.volume","43"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Vaiana, Andrea C."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2018-02-09T08:00:05Z"],["dc.date.available","2018-02-09T08:00:05Z"],["dc.date.issued","2015-08-18"],["dc.description.abstract","During ribosomal translation, the two ribosomal subunits remain associated through intersubunit bridges, despite rapid large-scale intersubunit rotation. The absence of large barriers hindering rotation is a prerequisite for rapid rotation. Here, we investigate how such a flat free-energy landscape is achieved, in particular considering the large shifts the bridges undergo at the periphery. The dynamics and energetics of the intersubunit contact network are studied using molecular dynamics simulations of the prokaryotic ribosome in intermediate states of spontaneous translocation. Based on observed occupancies of intersubunit contacts, residues were grouped into clusters. In addition to the central contact clusters, peripheral clusters were found to maintain strong steady interactions by changing contacts in the course of rotation. The peripheral B1 bridges are stabilized by a changing contact pattern of charged residues that adapts to the rotational state. In contrast, steady strong interactions of the B4 bridge are ensured by the flexible helix H34 following the movement of protein S15. The tRNAs which span the subunits contribute to the intersubunit binding enthalpy to an almost constant degree, despite their different positions in the ribosome. These mechanisms keep the intersubunit interaction strong and steady during rotation, thereby preventing dissociation and enabling rapid rotation."],["dc.identifier.doi","10.1093/nar/gkv649"],["dc.identifier.pmid","26109353"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/12081"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1362-4962"],["dc.title","Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

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[["dc.bibliographiccitation.firstpage","3a"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","110"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Vaiana, Andrea C."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:57:59Z"],["dc.date.available","2021-03-05T08:57:59Z"],["dc.date.issued","2016"],["dc.identifier.doi","10.1016/j.bpj.2015.11.061"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79958"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Low Energy Barriers and a Dynamic Contact Network between Ribosomal Subunits Enable Rapid tRNA Translocation"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

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[["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Schröder, Gunnar F."],["dc.contributor.author","Davydov, Iakov I."],["dc.contributor.author","Fischer, Niels"],["dc.contributor.author","Stark, Holger"],["dc.contributor.author","Rodnina, Marina V."],["dc.contributor.author","Vaiana, Andrea C."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2017-09-07T11:46:53Z"],["dc.date.available","2017-09-07T11:46:53Z"],["dc.date.issued","2014"],["dc.identifier.doi","10.1016/j.bpj.2013.11.2758"],["dc.identifier.eissn","1542-0086"],["dc.identifier.gro","3142197"],["dc.identifier.isi","000337000402731"],["dc.identifier.issn","0006-3495"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/5610"],["dc.language.iso","en"],["dc.notes","http://pubman.mpdl.mpg.de/pubman/faces/viewItemFullPage.jsp?itemId=escidoc:2049946:2"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Cell Press"],["dc.publisher.place","Cambridge"],["dc.relation.conference","58th Annual Meeting of the Biophysical-Society"],["dc.relation.eventend","2014-02-19"],["dc.relation.eventlocation","San Francisco, CA"],["dc.relation.eventstart","2014-02-15"],["dc.relation.ispartof","Biophysical Journal, 106(Supplement 1), 493a-493a."],["dc.title","Rapid and Stable Transfer RNA Translocation through the Ribosome Ensured by Specific Contact Mechanisms"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

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