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Institute for Advanced Simulation (IAS)
Journal Article - Online First
Can Constraint Network Analysis guide the identification phase of KnowVolution? A case study on improved thermostability of an endo-β-glucanase
Computational and structural biotechnology journal NA, S2001037020305596 (2020) [10.1016/j.csbj.2020.12.034]
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Journal Article - Online First
Targeting spectrin redox switches to regulate the mechanoproperties of red blood cells
Biological chemistry NA, NA (2020) [10.1515/hsz-2020-0293]
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Journal Article
The Puzzle of Metabolite Exchange and Identification of Putative Octotrico Peptide Repeat Expression Regulators in the Nascent Photosynthetic Organelles of Paulinella chromatophora
Frontiers in microbiology 11, 607182 (2020) [10.3389/fmicb.2020.607182]
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Journal Article
Cumulative Submillisecond All-Atom Simulations of the Temperature-Induced Coil-to-Globule Transition of Poly( N -vinylcaprolactam) in Aqueous Solution
Macromolecules 53(22), 9793–9810 (2020) [10.1021/acs.macromol.0c01896]
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Journal Article
Automated and optimally FRET-assisted structural modeling
Nature Communications 11(1), 5394 (2020) [10.1038/s41467-020-19023-1]
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Journal Article
Loop 1 of APOBEC3C regulates its antiviral activity against HIV-1
Journal of molecular biology 432(23), 6200-6227 (2020) [10.1016/j.jmb.2020.10.014]
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Journal Article
Semisynthetic Analogs of the Antibiotic Fidaxomicin—Design, Synthesis, and Biological Evaluation
ACS medicinal chemistry letters 11(12), 2414–2420 (2020) [10.1021/acsmedchemlett.0c00381]
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Journal Article
Characterization of the nucleotide-binding domain NsrF from the BceAB-type ABC-transporter NsrFP from the human pathogen Streptococcus agalactiae
Scientific reports 10(1), 15208 (2020) [10.1038/s41598-020-72237-7]
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Journal Article
Cell type-dependent escape of capsid inhibitors by simian immunodeficiency virus SIVcpz
Journal of virology 94(23), e01338-20 (2020) [10.1128/JVI.01338-20]
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Journal Article
Mechanism of fully-reversible, pH-sensitive inhibition of human glutamine synthetase by tyrosine nitration
Journal of chemical theory and computation 16(7), 4694–4705 (2020) [10.1021/acs.jctc.0c00249]
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Journal Article
AMBER-DYES in AMBER: Implementation of fluorophore and linker parameters into AmberTools
The journal of chemical physics 152(22), 221103 - (2020) [10.1063/5.0007630]
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Journal Article
Binding Modes of Thioflavin T and Congo Red to the Fibril Structure of Amyloid-β(1–42)
Chemical communications 56, 7589-7592 (2020) [10.1039/D0CC01161D]
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Journal Article
Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins
Nature Communications 11(1), 1725 (2020) [10.1038/s41467-020-15441-3]
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Journal Article
Fluorophore-labeled cyclic nucleotides as potent agonists of cyclic nucleotide-regulated ion channels
ChemBioChem 21(16), 2311-2320 (2020) [10.1002/cbic.202000116]
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Journal Article
Evidence for functional selectivity in TUDC- and norUDCA-induced signal transduction via α5β1 integrin towards choleresis
Scientific reports 10(1), 5795 (2020) [10.1038/s41598-020-62326-y]
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Journal Article
Resolving dynamics and function of transient states in single enzyme molecules
Nature Communications 11(1), 1231 (2020) [10.1038/s41467-020-14886-w]
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Contribution to a conference proceedings/Contribution to a book
Simulating Thioflavin T and Congo Red Binding to the Fibril Structure of Amyloid-$ß$(1-42)
NIC Symposium 2020
NIC Symposium 2020, JülichJülich, Germany, 27 Feb 2020 - 28 Feb 2020
Jülich : Forschungszentrum Jülich GmbH Zentralbibliothek, Verlag, Publication Series of the John von Neumann Institute for Computing (NIC) NIC Series 50, 53 - 61 (2020)
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Journal Article
Structural and dynamic insights revealing how lipase binding domain MD1 of Pseudomonas aeruginosa foldase affects lipase activation
Scientific reports 10(1), 3578 (2020) [10.1038/s41598-020-60093-4]
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Journal Article
TopModel: Template-based protein structure prediction at low sequence identity using top-down consensus and deep neural networks
Journal of chemical theory and computation 16(3), 1953-1967 (2020) [10.1021/acs.jctc.9b00825]
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Journal Article
Systematically scrutinizing the impact of substitution sites on thermostability and detergent tolerance for Bacillus subtilis lipase A
Journal of chemical information and modeling 60(3), 1568-1584 (2020) [10.1021/acs.jcim.9b00954]
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Journal Article
Dimerization energetics of the G‐protein coupled bile acid receptor TGR5 from all‐atom simulations
Journal of computational chemistry 41(9), 874-884 (2020) [10.1002/jcc.26135]
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Journal Article
The Membrane-Integrated Steric Chaperone Lif Facilitates Active Site Opening of Pseudomonas aeruginosa Lipase A
Journal of computational chemistry 4(6), 500-512 (2020) [10.1002/jcc.26085]
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Journal Article
Automated and Optimally FRET-Assisted Structural Modeling
Biophysical journal 116(3, Suppl 1) 333a - (2019) [10.1016/j.bpj.2018.11.1815]
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Journal Article
Synthesis of peptoid-based class I selective histone deacetylase inhibitors with chemosensitizing properties
Journal of medicinal chemistry 62(24), 11260-11279 (2019) [10.1021/acs.jmedchem.9b01489]
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Journal Article
Surprising Non-Additivity of Methyl-Groups in Drug-Kinase Interaction
ACS chemical biology 14(12), 2585-2594 (2019) [10.1021/acschembio.9b00476]
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Journal Article
N 6 -modified cAMP derivatives that activate protein kinase A also act as full agonists of murine HCN2 channels
The journal of biological chemistry 294, 17978-17987 (2019) [10.1074/jbc.RA119.010246]
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Journal Article
Basal Histamine H4 Receptor Activation: Agonist Mimicry by the Diphenylalanine Motif
Chemistry - a European journal 25(64), 14613-14624 (2019) [10.1002/chem.201902801]
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Journal Article
C-terminal Modulators of Heat Shock Protein of 90 kDa (HSP90): State of Development and Modes of Action
Bioorganic & medicinal chemistry 27(21), 115080 (2019) [10.1016/j.bmc.2019.115080]
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Journal Article
Small-molecule inhibitors of nisin resistance protein NSR from the human pathogen Streptococcus agalactiae
Bioorganic & medicinal chemistry 27(20), 115079 (2019) [10.1016/j.bmc.2019.115079]
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Journal Article
The tetrahydroxanthone-dimer phomoxanthone A is a strong inducer of apoptosis in cisplatin-resistant solid cancer cells
Bioorganic & medicinal chemistry 27(19), 115044 (2019) [10.1016/j.bmc.2019.115044]
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Journal Article
Fluorescent analogs of peptoid-based HDAC inhibitors: Synthesis, biological activity and cellular uptake kinetics
Bioorganic & medicinal chemistry 27(19), 115039 - (2019) [10.1016/j.bmc.2019.07.055]
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Journal Article
Partially inserted nascent chain unzips the lateral gate of the Sec translocon
EMBO reports 20, e48191 (2019) [10.15252/embr.201948191]
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Journal Article
Posttranslational modification of the NADP-malic enzyme involved in C4 photosynthesis fine-tunes the enzymatic activity during the day
The plant cell 31(10), 2525-2539 (2019) [10.1105/tpc.19.00406]
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Journal Article
Biallelic mutation of human SLC6A6 encoding the taurine transporter TAUT is linked to early retinal degeneration
The FASEB journal 33(10), 11507–11527 (2019) [10.1096/fj.201900914RR]
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Journal Article
Isoform-specific Inhibition of N-methyl-D-aspartate Receptors by Bile Salts
Scientific reports 9(1), 10068 (2019) [10.1038/s41598-019-46496-y]
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Journal Article
Structural Model of the ETR1 Ethylene Receptor Transmembrane Sensor Domain
Scientific reports 9(1), 8869 (2019) [10.1038/s41598-019-45189-w]
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Journal Article
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 (2019) [10.1021/acs.jcim.9b00269]
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Journal Article
Novel Fluorescent Cyclic Nucleotide Derivatives to Study CNG and HCN Channel Function
Biophysical journal 116(12), 2411-2422 (2019) [10.1016/j.bpj.2019.05.006]
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Journal Article
Calcium-promoted interaction between the C2-domain protein EHB1 and metal transporter IRT1 inhibits Arabidopsis iron acquisition
Plant physiology 180(3), 1564-1581 (2019) [10.1104/pp.19.00163]
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Journal Article
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 (2019) [10.1021/acs.jctc.8b01295]
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Journal Article
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 (2019) [10.3389/fphar.2019.00400]
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Journal Article
JAK2 p.G571S in B-cell precursor acute lymphoblastic leukemia: a synergizing germline susceptibility
Leukemia 33, 2331–2335 (2019) [10.1038/s41375-019-0459-z]
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Journal Article
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 (2019) [10.1107/S2053230X19002152]
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Journal Article
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 (2019) [10.1074/jbc.RA119.007656]
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Journal Article
Co-culture of the fungus Fusarium tricinctum with Streptomyces lividans induces production of cryptic naphthoquinone dimers
RSC Advances 9(3), 1491 - 1500 (2019) [10.1039/C8RA09067J]
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Journal Article
Nutrient exchange in arbuscular mycorrhizal symbiosis from a thermodynamic point of view
The new phytologist 222(2), 1043-1053 (2019) [10.1111/nph.15646]
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Journal Article
Converging a Knowledge-Based Scoring Function: DrugScore2018
Journal of chemical information and modeling 59(1), 509–521 (2019) [10.1021/acs.jcim.8b00582]
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Journal Article
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 (2019) [10.1128/AAC.01146-18]
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Journal Article
Design, Synthesis and Biological Evaluation of β-Peptoid-Capped HDAC Inhibitors with Anti-Neuroblastoma and Anti-Glioblastoma Activity
MedChemComm 10(7), 1109-1115 (2019) [10.1039/C8MD00454D]
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Journal Article
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 (2018) [10.1021/acs.jctc.8b00690]
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Journal Article
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 (2018) [10.1038/s41598-018-33050-5]
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Journal Article
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 (2018) [10.1016/j.cellsig.2018.06.015]
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Journal Article
Interaction of Ochratoxin A and Its Thermal Degradation Product 2′R-Ochratoxin A with Human Serum Albumin
Toxins 10(7), 256 - (2018) [10.3390/toxins10070256]
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Journal Article
Targeting HSP90 dimerization via the C-terminus is effective in imatinib resistant CML and lacks heat shock response
Blood 132(3), 307-320 (2018) [10.1182/blood-2017-10-810986]
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Journal Article
On the contributing role of the transmembrane domain for subunit-specific sensitivity of integrin activation
Scientific reports 8(1), 5733 (2018) [10.1038/s41598-018-23778-5]
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Journal Article
Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1
Scientific reports 8(1), 3890 (2018) [10.1038/s41598-018-21952-3]
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Contribution to a conference proceedings/Contribution to a book
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 2018
Jülich : John von Neumann Institute for Computing, Publication Series of the John von Neumann Institute for Computing (NIC) NIC Series 49, 25 - 31 (2018)
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Journal Article
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 (2018) [10.1074/jbc.RA118.002149]
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Journal Article
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 (2018) [10.1128/JVI.01697-17]
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Journal Article
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 (2017) [10.1186/s12934-017-0772-z]
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Journal Article
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 (2017) [10.1021/acs.jcim.7b00567]
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Journal Article
Rigidity theory for biomolecules: concepts, software, and applications
Wiley interdisciplinary reviews / Computational Molecular Science 7(4), e1311 (2017) [10.1002/wcms.1311]
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Journal Article
On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase
Scientific reports 7(1), 8020 (2017) [10.1038/s41598-017-08521-w]
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Journal Article
Lipid Transport by the ABC Transporter MDR3
Innovatives Supercomputing in Deutschland 15(1), 82-86 (2017)
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Journal Article
Force field dependence of riboswitch dynamics
Methods in enzymology 553, 163‐191 (2015) [10.1016/bs.mie.2014.10.056]
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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.
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)
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)
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)