Grubmüller, Helmut

[["dc.bibliographiccitation.artnumber","acs.jcim.2c00044"],["dc.bibliographiccitation.journal","Journal of Chemical Information and Modeling"],["dc.contributor.author","Kutzner, Carsten"],["dc.contributor.author","Kniep, Christian"],["dc.contributor.author","Cherian, Austin"],["dc.contributor.author","Nordstrom, Ludvig"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Gapsys, Vytautas"],["dc.date.accessioned","2022-04-01T10:01:40Z"],["dc.date.available","2022-04-01T10:01:40Z"],["dc.date.issued","2022"],["dc.identifier.doi","10.1021/acs.jcim.2c00044"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/105722"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-530"],["dc.relation.eissn","1549-960X"],["dc.relation.issn","1549-9596"],["dc.title","GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","139a"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","112"],["dc.contributor.author","Kutzner, Carsten"],["dc.contributor.author","Ullmann, R. Thomas"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Zachariae, Ulrich"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:58:01Z"],["dc.date.available","2021-03-05T08:58:01Z"],["dc.date.issued","2017"],["dc.identifier.doi","10.1016/j.bpj.2016.11.769"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79973"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Ions in Action - Studying Ion Channels by Computational Electrophysiology in GROMACS"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","680a"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","114"],["dc.contributor.author","Buelens, Floris P."],["dc.contributor.author","Leonov, Hadas"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:58:03Z"],["dc.date.available","2021-03-05T08:58:03Z"],["dc.date.issued","2018"],["dc.identifier.doi","10.1016/j.bpj.2017.11.3668"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79984"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","ATP as a Fuel Molecule: Evolutionary Selection of Magnesium-ATP Interaction Mode Facilitates Lossless Chemomechanical Coupling for ATPases"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","8281"],["dc.bibliographiccitation.issue","19"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","8290"],["dc.bibliographiccitation.volume","39"],["dc.contributor.author","Seeliger, Daniel"],["dc.contributor.author","Buelens, Floris P."],["dc.contributor.author","Goette, Maik"],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2017-09-07T11:43:22Z"],["dc.date.available","2017-09-07T11:43:22Z"],["dc.date.issued","2011"],["dc.description.abstract","DNA-binding proteins are key players in the regulation of gene expression and, hence, are essential for cell function. Chimeric proteins composed of DNA-binding domains and DNA modifying domains allow for precise genome manipulation. A key prerequisite is the specific recognition of a particular nucleotide sequence. Here, we quantitatively assess the binding affinity of DNA-binding proteins by molecular dynamics-based alchemical free energy simulations. A computational framework was developed to automatically set up in silico screening assays and estimate free energy differences using two independent procedures, based on equilibrium and non-equlibrium transformation pathways. The influence of simulation times on the accuracy of both procedures is presented. The binding specificity of a zinc-finger transcription factor to several sequences is calculated, and agreement with experimental data is shown. Finally we propose an in silico screening strategy aiming at the derivation of full specificity profiles for DNA-binding proteins."],["dc.identifier.doi","10.1093/nar/gkr531"],["dc.identifier.gro","3142657"],["dc.identifier.isi","000296341100009"],["dc.identifier.pmid","21737424"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/85"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10 / Funder: Deutsche Forschungsgemeinschaft (DFG) [GR 2079/4-1]; Max Planck Society"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0305-1048"],["dc.title","Towards computional specificity screening of DNA-binding proteins"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","71"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Methods"],["dc.bibliographiccitation.lastpage","73"],["dc.bibliographiccitation.volume","14"],["dc.contributor.author","Huang, Jing"],["dc.contributor.author","Rauscher, Sarah"],["dc.contributor.author","Nawrocki, Grzegorz"],["dc.contributor.author","Ran, Ting"],["dc.contributor.author","Feig, Michael"],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","MacKerell, Alexander D."],["dc.date.accessioned","2017-09-07T11:52:30Z"],["dc.date.available","2017-09-07T11:52:30Z"],["dc.date.issued","2016"],["dc.identifier.doi","10.1038/nmeth.4067"],["dc.identifier.gro","3144938"],["dc.identifier.pii","BFnmeth4067"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2617"],["dc.language.iso","en"],["dc.notes.intern","Crossref Import"],["dc.notes.status","final"],["dc.relation.eissn","1548-7105"],["dc.relation.issn","1548-7091"],["dc.rights.uri","http://www.springer.com/tdm"],["dc.title","CHARMM36m: an improved force field for folded and intrinsically disordered proteins"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","987"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Journal of Molecular Biology"],["dc.bibliographiccitation.lastpage","994"],["dc.bibliographiccitation.volume","300"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Heymann, J. B."],["dc.contributor.author","Engel, A."],["dc.contributor.author","Mitsuoka, K."],["dc.contributor.author","Fujiyoshi, Y."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2017-09-07T11:46:48Z"],["dc.date.available","2017-09-07T11:46:48Z"],["dc.date.issued","2000"],["dc.description.abstract","The fold of human aquaporin 1 is determined from cryo-electron microscopic data at 4.5 Angstrom resolution. The monomeric structure consists of two transmembrane triple helices arranged around a pseudo-2-fold axis connected by a long flexible extracellular loop. Each triplet contains between its second and third helix a functional loop containing the highly conserved fingerprint NPA motif. These functional loops are assumed to fold inwards between the two triplets, thereby forming the heart of the water channel. The helix topology was determined from the directionality pattern of each of the six transmembrane helices with respect to the membrane, together with constraints defined by the sequence and atomic force microscopy data. The directionality of the helices was determined by collecting the best-fitting orientations resulting from a search through the three-dimensional experimental map for a large number of alpha-helical fragments. Tests on cryo-electron crystallographic bacteriorhodopsin data suggest that our method is generally applicable to determine the topology of helical proteins for which only medium-resolution electron microscopy data are available."],["dc.identifier.doi","10.1006/jmbi.2000.3913"],["dc.identifier.gro","3144371"],["dc.identifier.isi","000088508500024"],["dc.identifier.pmid","10891283"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/1987"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0022-2836"],["dc.title","The fold of human aquaporin 1"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1433"],["dc.bibliographiccitation.journal","Biochemical Society transactions"],["dc.bibliographiccitation.lastpage","1437"],["dc.bibliographiccitation.volume","36"],["dc.contributor.author","Lakomek, Nils-Alexander"],["dc.contributor.author","Lange, Oliver F."],["dc.contributor.author","Walter, Korvin F. A."],["dc.contributor.author","Farès, Christophe"],["dc.contributor.author","Egger, Dalia"],["dc.contributor.author","Lunkenheimer, Peter"],["dc.contributor.author","Meiler, Jens"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Griesinger, Christian"],["dc.date.accessioned","2017-09-07T11:48:08Z"],["dc.date.available","2017-09-07T11:48:08Z"],["dc.date.issued","2008"],["dc.description.abstract","RDCs (residual dipolar couplings) in NMR spectroscopy provide information about protein dynamics complementary to NMR relaxation methods, especially in the previously inaccessible time window between the protein correlation time tau(c), and 50 mu s. For ubiquitin, new modes of motion of the protein backbone could be detected using RDC-based techniques. An ensemble of ubiquitin based on these RDC values is found to comprise all different conformations that ubiquitin adopts upon binding to different recognition proteins. These conformations in protein-protein complexes had been derived from 46 X-ray structures. Thus, for ubiquitin recognition by other proteins, conformational selection rather than induced fit seems to be the dominant mechanism."],["dc.identifier.doi","10.1042/BST0361433"],["dc.identifier.gro","3143198"],["dc.identifier.isi","000261749200066"],["dc.identifier.pmid","19021570"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/686"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0300-5127"],["dc.title","Residual dipolar couplings as a tool to study molecular recognition of ubiquitin"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","663"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Pflügers Archiv European Journal of Physiology"],["dc.bibliographiccitation.lastpage","669"],["dc.bibliographiccitation.volume","456"],["dc.contributor.author","Mueller, E. Matthias"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Groot, Bert L. de"],["dc.date.accessioned","2017-09-07T11:48:16Z"],["dc.date.available","2017-09-07T11:48:16Z"],["dc.date.issued","2008"],["dc.description.abstract","Excessive water uptake through aquaporins can be life threatening, and disregulation of water permeability causes many diseases. Therefore, reversible aquaporin inhibitors are highly desired. In this paper, we identified the binding site for tetraethylammonium (TEA) of the membrane water channel aquaporin-1 by a combined molecular docking and molecular dynamics simulation approach. The binding site identified from docking studies was independently confirmed with an unbiased molecular dynamics simulation of an aquaporin tetramer embedded in a lipid membrane, surrounded by a 100-mM tetraethylammonium solution in water. A third independent assessment of the binding site was obtained by umbrella sampling simulations. These simulations, in addition, revealed a binding affinity of more than 17kJ/mol, corresponding to an IC50 value of << 3mM. Finally, we observed in our simulations a 50% reduction of the water flux in the presence of TEA, in agreement with water permeability measurements on aquaporin expressed in oocytes. These results confirm TEA as a putative lead for an aquaporin-1 inhibitor."],["dc.identifier.doi","10.1007/s00424-007-0422-0"],["dc.identifier.gro","3143275"],["dc.identifier.isi","000255866800003"],["dc.identifier.pmid","18196268"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/771"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1432-2013"],["dc.relation.issn","0031-6768"],["dc.title","Is TEA an inhibitor for human aquaporin-1?"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","299"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Journal of Molecular Biology"],["dc.bibliographiccitation.lastpage","313"],["dc.bibliographiccitation.volume","309"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Daura, X."],["dc.contributor.author","Mark, A. E."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2017-09-07T11:46:07Z"],["dc.date.available","2017-09-07T11:46:07Z"],["dc.date.issued","2001"],["dc.description.abstract","A principal component analysis has been applied on equilibrium simulations of a beta -heptapeptide that shows reversible folding in a methanol solution. The analysis shows that the configurational space contains only three dense sub-states. These states of relatively low free energy correspond to the \"native\" left-handed helix, a partly helical intermediate, and a hairpin-like structure. The collection of unfolded conformations form a relatively diffuse cloud with little substructure, Internal hydrogen-bonding energies were found to correlate well with the degree of folding. The native helical structure folds from the N terminus; the transition from the major folding intermediate to the native helical structure involves the formation of the two most C-terminal backbone hydrogen bonds. A four-state Markov model was found to describe transition frequencies between the conformational states within error limits, indicating that memory-effects are negligible beyond the nanosecond time-scale. The dominant native state fluctuations were found to be very similar to unfolding motions, suggesting that unfolding pathways can be inferred from fluctuations in the native state. The low-dimensional essential subspace, describing 69% of the collective atomic fluctuations, was found to converge at time-scales of the order of one nanosecond at all temperatures investigated, whereas folding/unfolding takes place at significantly longer time-scales, even above the melting temperature."],["dc.identifier.doi","10.1006/jmbi.2001.4655"],["dc.identifier.gro","3144283"],["dc.identifier.isi","000169034800023"],["dc.identifier.pmid","11491298"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/1890"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0022-2836"],["dc.title","Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","404"],["dc.bibliographiccitation.lastpage","405"],["dc.bibliographiccitation.seriesnr","4192"],["dc.contributor.author","Kutzner, Carsten"],["dc.contributor.author","Van der Spoel, David"],["dc.contributor.author","Fechner, Martin"],["dc.contributor.author","Lindahl, Erik"],["dc.contributor.author","Schmitt, Udo W."],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.editor","Träff, Jesper Larsson"],["dc.contributor.editor","Mohr, Bernd"],["dc.contributor.editor","Worringen, Joachim"],["dc.contributor.editor","Dongarra, Jack"],["dc.date.accessioned","2017-09-07T11:52:33Z"],["dc.date.available","2017-09-07T11:52:33Z"],["dc.date.issued","2006"],["dc.description.abstract","We investigated the prerequisites for decent scaling of the GROMACS 3.3 molecular dynamics (MD) code [1] on Ethernet Beowulf clusters. The code uses the MPI standard for communication between the processors and scales well on shared memory supercomputers like the IBM p690 (Regatta) and on Linux clusters with a high-bandwidth/low latency network. On Ethernet switched clusters, however, the scaling typically breaks down as soon as more than two computational nodes are involved. For an 80k atom MD test system, exemplary speedups Sp N on N CPUs are Sp 8 = 6.2, Sp 16 = 10 on a Myrinet dual-CPU 3 GHz Xeon cluster, Sp 16 = 11 on an Infiniband dual-CPU 2.2 GHz Opteron cluster, and Sp 32 = 21 on one Regatta node. However, the maximum speedup we could initially reach on our Gbit Ethernet 2 GHz Opteron cluster was Sp 4 = 3 using two dual-CPU nodes. Employing more CPUs only led to slower execution (Table 1)."],["dc.identifier.doi","10.1007/11846802_57"],["dc.identifier.gro","3144948"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2629"],["dc.language.iso","en"],["dc.notes.intern","Crossref Import"],["dc.notes.status","final"],["dc.relation.crisseries","Lecture Notes in Computer Science"],["dc.relation.isbn","978-3-540-39110-4"],["dc.relation.ispartof","Recent Advances in Parallel Virtual Machine and Message Passing Interface"],["dc.relation.ispartofseries","LLecture Notes in Computer Science book series; 4192"],["dc.relation.issn","0302-9743"],["dc.title","Improved GROMACS Scaling on Ethernet Switched Clusters"],["dc.type","book_chapter"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dspace.entity.type","Publication"]]