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Publications of the NIC Research Group
since April 2017

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PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein–Lipid-Bilayer System Building
Journal of chemical information and modeling 59(6), 2522-2528 () [10.1021/acs.jcim.9b00269] Embargoed OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Novel Fluorescent Cyclic Nucleotide Derivatives to Study CNG and HCN Channel Function
Biophysical journal 116(12), 2411-2422 () [10.1016/j.bpj.2019.05.006] Embargoed OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Calcium-promoted interaction between the C2-domain protein EHB1 and metal transporter IRT1 inhibits Arabidopsis iron acquisition
Plant physiology 180(3), 1564-1581 () [10.1104/pp.19.00163]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Cosolvent-enhanced Sampling and Unbiased Identification of Cryptic Pockets Suitable for Structure-based Drug Design
Journal of chemical theory and computation 15(5), 3331–3343 () [10.1021/acs.jctc.8b01295] Embargoed OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Novel 3,4-Dihydroisocoumarins Inhibit Human P-gp and BCRP in Multidrug Resistant Tumors and Demonstrate Substrate Inhibition of Yeast Pdr5
Frontiers in pharmacology 10, 400 () [10.3389/fphar.2019.00400] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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JAK2 p.G571S in B-cell precursor acute lymphoblastic leukemia: a synergizing germline susceptibility
Leukemia NA, NA () [10.1038/s41375-019-0459-z]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Pseudomonas aeruginosa esterase PA2949, a bacterial homolog of the human membrane esterase ABHD6: expression, purification and crystallization
Acta crystallographica / F Structural biology communications Section F F75(4), 270 - 277 () [10.1107/S2053230X19002152] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Phosphorylated tyrosine 93 of hepatitis C virus nonstructural protein 5A is essential for interaction with host c-Src and efficient viral replication
The journal of biological chemistry 294, 7388-7402 () [10.1074/jbc.RA119.007656]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Co-culture of the fungus Fusarium tricinctum with Streptomyces lividans induces production of cryptic naphthoquinone dimers
RSC Advances 9(3), 1491 - 1500 () [10.1039/C8RA09067J] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Nutrient exchange in arbuscular mycorrhizal symbiosis from a thermodynamic point of view
The new phytologist 222(2), 1043-1053 () [10.1111/nph.15646]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Converging a Knowledge-Based Scoring Function: DrugScore2018
Journal of chemical information and modeling 59(1), 509–521 () [10.1021/acs.jcim.8b00582] Embargoed OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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FK506 resistance of Saccharomyces cerevisiae Pdr5 and Candida albicans Cdr1 involves mutations in the transmembrane domains and extracellular loops
Antimicrobial agents and chemotherapy 63(1), e01146-18 () [10.1128/AAC.01146-18] Embargoed OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Design, Synthesis and Biological Evaluation of β-Peptoid-Capped HDAC Inhibitors with Anti-Neuroblastoma and Anti-Glioblastoma Activity
MedChemComm N/A, n/a () [10.1039/C8MD00454D]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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TopScore: Using Deep Neural Networks and Large Diverse Data Sets for Accurate Protein Model Quality Assessment
Journal of chemical theory and computation 14(11), 6117–6126 () [10.1021/acs.jctc.8b00690]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Hydrophobic alkyl chains substituted to the 8-position of cyclic nucleotides enhance activation of CNG and HCN channels by an intricate enthalpy - entropy compensation
Scientific reports 8(1), 14960 () [10.1038/s41598-018-33050-5] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Relevance of N-terminal residues for amyloid-β binding to platelet integrin α IIb β 3 , integrin outside-in signaling and amyloid-β fibril formation
Cellular signalling 50, 121 - 130 () [10.1016/j.cellsig.2018.06.015]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Interaction of Ochratoxin A and Its Thermal Degradation Product 2′R-Ochratoxin A with Human Serum Albumin
Toxins 10(7), 256 - () [10.3390/toxins10070256] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Targeting HSP90 dimerization via the C-terminus is effective in imatinib resistant CML and lacks heat shock response
Blood 132(3), 307-320 () [10.1182/blood-2017-10-810986] BibTeX | EndNote: XML, Text | RIS

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On the contributing role of the transmembrane domain for subunit-specific sensitivity of integrin activation
Scientific reports 8(1), 5733 () [10.1038/s41598-018-23778-5] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1
Scientific reports 8(1), 3890 () [10.1038/s41598-018-21952-3] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Unravelling the Di- and Oligomerisation Interfaces of the G-Protein Coupled Bile Acid Receptor TGR5 via Integrative Modelling
NIC Symposium 2018, JülichJülich, Germany, 22 Feb 2018 - 23 Feb 20182018-02-222018-02-23 Jülich : John von Neumann Institute for Computing, Publication Series of the John von Neumann Institute for Computing (NIC) NIC Series 49, 25 - 31 () OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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The human platelet antigen-1b variant of $\alpha$$_{IIb}$β$_{3}$ allosterically shifts the dynamic conformational equilibrium of this integrin toward the active state
The journal of biological chemistry 293, 4830-4844 () [10.1074/jbc.RA118.002149] Embargoed OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Identification of a Conserved Interface of Human Immunodeficiency Virus Type 1 and Feline Immunodeficiency Virus Vifs with Cullin 5
Journal of virology 92(6), e01697-17 () [10.1128/JVI.01697-17] Embargoed OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Contribution of single amino acid and codon substitutions to the production and secretion of a lipase by Bacillus subtilis
Microbial cell factories 16(1), 160 () [10.1186/s12934-017-0772-z] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Tertiary Interactions in the Unbound Guanine-Sensing Riboswitch Focus Functional Conformational Variability on the Binding Site
Journal of chemical information and modeling 57(11), 2822–2832 () [10.1021/acs.jcim.7b00567]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Rigidity theory for biomolecules: concepts, software, and applications
Wiley interdisciplinary reviews / Computational Molecular Science 7(4), e1311 () [10.1002/wcms.1311] BibTeX | EndNote: XML, Text | RIS

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On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase
Scientific reports 7(1), 8020 () [10.1038/s41598-017-08521-w] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Lipid Transport by the ABC Transporter MDR3
Innovatives Supercomputing in Deutschland 15(1), 82-86 () OpenAccess  Download fulltext Files  Download fulltextFulltext Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Publications of NIC Research Group-related projects or NIC computing time projects

2017

Pfleger, C., Minges, A., Boehm, M., McClendo, C.L., Torella, R., Gohlke, H.
Ensemble- and rigidity theory-based perturbation approach to analyze dynamic allostery
J. Chem. Theory Comput., accepted, 2017, DOI: 10.1021/acs.jctc.7b00529
(NIC project ID. HDD17)

Skoczinski, P., Volkenborn, K., Fulton, A., Bhadauriya, A., Nutschel, C., Gohlke, H., Knapp, A., Jaeger, K.-E.
Contribution of single amino acid and codon substitutions to the production and secretion of a lipase by Bacillus subtilis.
Microb. Cell Fact. 2017, 16, 160.

Dick, M., Erlenkamp, G., Nguyen, G.T.T., Förster, K., Groth, G., Gohlke, H.
Pyrazolidine-3,5-dione-based inhibitors of phosphoenolpyruvate carboxylase as new class of potential C4 plant herbicides.
FEBS Lett. 2017, DOI: 10.1002/1873-3468.12842.

Dröge, C., Bonus, M., Baumann, U., Klindt, C.,Lainka, E., Kathemann, S., Brinkert, F., Grabhorn, E., Wenning, D., Fichtner, A., Gotthardt, D.N., Weiss, K.H., McKiernan, P., Puri, R.D., Verma, I.C., Kluge, S., Gohlke, H., Schmitt, L., Kubitz, R., Häussinger, D., Keitel, V.
Sequencing of FIC1, BSEP and MDR3 in 427 unrelated patients with cholestasis revealed 154 different genetic variants.
J. Hepatol. 2017, DOI: 10.1016/j.jhep.2017.07.004.
(NIC project ID: HDU19)

Hanke, C.A., Gohlke, H.
Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch.
PLOS ONE 2017, 12, e0179271. [PDF]
(NIC project ID: HDD08)

Minges, A.R.M, Ciupka, D., Winkler, C., Höppner, A., Gohlke, H., Groth, G.
Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase.
Sci. Rep. 2017, 7, 45389. [PDF]
(NIC project ID: HDD14).

Kroeger, T., Frieg, B., Zhang, T., Hansen, F.K., Marmann, A., Proksch, P., Nagel-Steger, L., Groth, G., Smits, S.H.J., Gohlke, H.
EDTA aggregates induce SYPRO Orange-based fluorescence in thermal shift assay.
PLOS ONE 2017, 12, e0177024.

2016

Greife, A., Felekyan, S., Ma, Q., Gertzen, C.G.W., Spomer, L., Dimura, M., Peulen, T.O., Wöhler, C., Häussinger, D., Gohlke, H., Keitel, V., Seidel, C.A.M.
Structural assemblies of the di- and oligomeric G-protein coupled receptor TGR5 in live cells: an MFIS-FRET and integrative modeling study.
Sci. Rep. 2016, 6, 36792.
(NIC project ID: HDD15).

Donner, L., Fälker, K., Gremer, L., Klinker, S., Pagani, G., Ljungberg, L.U., Lothmann, K., Rizzi, F., Schaller, M., Gohlke, H., Willbold, D., Grenegard, M., Elvers, M.
Blood platelets contribute to the formation of amyloid deposits in cerebral vessels via integrin alphaIIbbeta3 induced outside-in signaling and clusterin release.
Sci. Signal. 2016, 9, RA52.
(NIC project ID: HDD11)

Frieg, B., Görg, B., Homeyer, N., Keitel, V., Häussinger, D., Gohlke, H.
Molecular mechanisms of glutamine synthetase mutations that lead to clinically relevant pathologies.
PLOS Comp. Biol. 2016, 12, e1004693.
(NIC project ID: HDD13)

2015

Hanke, C.A., Gohlke, H.
Force field dependence of riboswitch dynamics.
in: "Computational methods for understanding riboswitches", S.-J. Chen and D.H. Burke-Aguero (eds.), Vol. 553, MIE, Academic Press, 2015, 163-191.
(NIC project ID: HDD08)

Fulle, S., Saini, J.S., Homeyer, N., Gohlke, H.
Complex long-distance effects of mutations that confer linezolid resistance in the large ribosomal subunit.
Nucleic Acids Res. 2015, 43, 7731–7743.
(NIC project ID: HDD05)

2013

Saini, J.S., Homeyer, N., Fulle, S., Gohlke, H.
Determinants of the species-selectivity of oxazolidinone antibiotics targeting the large ribosomal subunit.
Biol. Chem. 2013, 394, 1529-1541.
(NIC project ID: HDD05)


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