Full Papers and Book Chapters

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2019


208. Wäschenbach, L., Gertzen, C.G.W., Keitel V., Gohlke H.
Dimerization energetics of the G-protein coupled bile acid receptor TGR5 from all-atom simulations.
Submitted 2019.
207. Verma, N., Dollinger, P., Kovacic, F., Jaeger, K.-E., Gohlke, H.
The membrane-integrated steric chaperone Lif facilitates active site opening of Pseudomonas aeruginosa lipase A.
Submitted 2019.
206. Schmidt-Wienen, B., Schmidt, D., Gerber, H.-D., Heine, A., Gohlke, H., Klebe, G.
Surprising non-additivity of methyl-groups in drug-kinase interaction.
Submitted 2019.
205. Bickel, D., Gohlke, H.
C-terminal modulators of heat shock protein of 90 kDa (HSP90): State of development and modes of action.
Submitted 2019.
204. Wang, C., Engelke, L., Bickel, D., Hamacher, A., Frank, M., Proksch, P., Gohlke, H., Kassack, M.U.
The tetrahydroxanthone-dimer phomoxanthone A is a strong inducer of apoptosis in cisplatin-resistant solid cancer cells.
Submitted 2019.
203. Porta, N., Zaschke-Kriesche, J., Frieg, B., Gopalswamy, M., Zivkovic, A., Etzkorn, M., Stark, H., Smits, S.H.J., Gohlke, H.
Small-molecule inhibitors of nisin resistance protein NSR from the human pathogen Streptococcus agalactiae.
Submitted 2019.
202. Wifling, D., Pfleger, C., Kaindl, J., Ibrahim, P., Kling, R.C., Buschauer, A., Gohlke, H., Clark, T.
Basal histamine H4 receptor activation: Agonist mimicry by the diphenylalanine motif.
Submitted 2019.
201. Raudszus, R., Nowothy, R., Gertzen, C.G.W., Schöler, A., Krizsan, A., Gockel, I., Kalwa, H., Gohlke, H., Thieme, R., Hansen, F.K.
Fluorescent analogs of peptoid-based HDAC inhibitors: synthesis, biological activity and cellular uptake kinetics.
Submitted 2019.
200. Kalinin, S., Fulle, S., Kuehnemuth, R., Sindbert, S., Felekyan, S., Gohlke, H., Seidel, C.A.M.
Diffusion with traps: Experiment, simulation, and theory to describe the dynamics of flexibly linked fluorophores in biomolecular FRET.
Submitted 2019.
199. Viegas, A., Dollinger, P., Verma, N., Seidel, C., Gohlke, H., Etzkorn, M., Kovacic, F., Jaeger, K.-E.
Solution NMR structure of lipase binding domain MD1 of Pseudomonas aeruginosa foldase and its potential role in lipase folding.
Submitted 2019.
198. Xu, H.C., Huang, J., Pandyra, A.A., Wang, R., Zhang, Z., Zhuang, Y., Gertzen, C.G.W., Geist, N., Münk, C., Herebian, D., Recher, M., Gohlke, H., Häussinger, D., Lang, K.S., Lang, P.A.
MHC-I silences virus specific CD8+ T cells to prevent immunopathology.
Submitted 2019.
197. Frieg, B., Görg, B., Qvartskhava, N., Jeitner, T., Homeyer, N., Häussinger, D., Gohlke, H.
Mechanism of fully-reversible, pH-sensitive inhibition of human glutamine synthetase by tyrosine nitration.
Submitted 2019.
196. Peulen, T.O., Hengstenberg, C.S., Biehl, R., Dimura, M., Lorenz, C., Valeri, A., Ince, S., Vöpel, T., Faragó, B., Gohlke, H., Klare, J.P., Stadler, A., Seidel, C.A.M., Herrmann, C.
An integrative approach maps motions and conformers essential for oligomerization of the large GTPase hGBP1.
Submitted 2019.
195. Dimura, M., Peulen, T.O., Sanabria, H., Rodnin, D., Hemmen, K., Seidel, C.A.M., Gohlke, H.
Automated and optimally FRET-assisted structural modeling.
Submitted 2019.
194. Bonus, M., Sommerfeld, A., Qvartskhava, N., Görg, B., Ludwig, B.S., Kessler, H., Gohlke, H., Häussinger, D.
Evidence for functional selectivity in TUDC- and norUDCA-induced signal transduction via α5β1 integrin towards choleresis.
Submitted 2019.
193. Form, I., Daletos, G., Bonus, M., Gohlke, H., Proksch, P.
Xanthone-, quinone-, benzophenone- and bianthrone-derivatives from the hypersaline lake soil-derived fungus Aspergillus wentii.
Bioorg. Med. Chem. 2019, in press.
192.
Bovdilova, A., Alexandre, B.M., Alvarez, C.E., Matias Luís, I., Höppner, A., Bickel, D., Gohlke, H., Nagel-Steger, L., Trajtenberg, F., Buschiazzo, A., Alseekh, S., Fernie, A., Drincovich, M.F., Abreu, I.A., Maurino, V.G.
Posttranslational modification of the NADP-malic enzyme involved in C4 photosynthesis fine-tunes the enzymatic activity during the day.
Plant Cell 2019, accepted.
191. Kater, L., Frieg, B., Berninghausen, O., Gohlke, H., Beckmann, R., Kedrov, A.
Partially inserted nascent chain unzips the lateral gate of the translocon.
EMBO Rep. 2019, accepted.
190. Preising, M.N., Görg, B., Friedburg, C., Qvartskhava, N., Budde, B.S., Bonus, M., Toliat, M.R., Pfleger, C., Altmüller, J., Herebian, D., Beyer, M., Zöllner, H., Wittsack, H.-J., Schaper, J., Klee, D., Zechner, U., Nürnberg, P., Schipper, J., Schnitzler, A., Gohlke, H., Lorenz, B., Häussinger, D., Bolz, H.J.
Biallelic mutation of SLC6A6 (TAUT) causes taurine deficiency and early retinal degeneration.
FASEB J. 2019, in press.
189. Koch, A., Bonus, M., Gohlke, H., Klöcker, N.
Isoform-specific inhibition of NMDARs by human bile acids.
Sci. Rep. 2019,  9, 10068. [PDF]
188. Keitel, V., Gertzen, C.G.W., Spomer, L., Gohlke. H., Häussinger, D.
Chapter 21: TGR5 (GPBAR1) in the liver.
6th edition of The Liver – Biology and Pathobiology, eds. Arias, I., Alter, H., Boyer, J., Cohen, D., Torgeirsson, S., Shafritz, D., Wolkoff, A., 2019.
187. Schott-Verdugo, S., Müller, L., Classen, E., Gohlke, H., Groth, G.
Structural model of the ETR1 ethylene receptor transmembrane sensor domain.
Sci. Rep. 2019, 9, 8869. [PDF]
186. Schott-Verdugo, S., Gohlke, H.
PACKMOL-Memgen: A simple-to-use generalized workflow for membrane-protein/lipid-bilayer system building.
J. Chem. Inf. Model. 2019, 59, 6, 2522-2528. [PDF]
185. Otte, M., Schweinitz, A., Lelle, M., Thon, S., Enke, U., Schmauder, R., Bonus, M., Gohlke, H., Benndorf, K.
Novel fluorescent cyclic nucleotide derivatives to study CNG and HCN channel function.
Biophys. J. 2019,  16, 2411-2422. [PDF]
184. Schmidt, D., Boehm, M., McClendon, C.L., Torella, R., Gohlke, H.
Cosolvent-enhanced sampling and unbiased identification of cryptic pockets suitable for structure-based drug design.
J. Chem. Theory Comput. 2019, 15, 3331-3343. [PDF]
183. Khan, I., Gratz, R., Denezhkin, P., Schott-Verdugo, S., Angrand, K., Genders, L., Basgaran, R.M., Fink-Straube, C., Brumbarova, T., Gohlke, H., Bauer, P., Ivanov, R.
Calcium-promoted interaction between peripheral membrane protein EHB1 and metal transporter IRT1 inhibits Arabidopsis iron acquisition.
Plant Physiol. 2019, pp.00163.2019. [PDF]
182. Sachs, J., Döhl, K., Weber, A., Bonus, M., Blesse, F., Fleischer, E., Klinger, A., Gohlke, H., Pietruszka, J., Schmitt, L., Teusch, N.E.
Novel 3,4-Dihydroisocoumarins Inhibit Human P-gp and BCRP in Multidrug Resistant Tumors and Demonstrate Substrate Inhibition of Yeast Pdr5.
Front. Pharmacol. 2019, 10, 400. [PDF]
181. Lin, M., Nebral, K., Gertzen, C.G.W., Ganmore, I., Haas, O.A., Bathia, S., Fischer, U., Kuhlen, M., Gohlke, H., Izraeli, S., Trka, J., Hu, J., Borkhardt, A., Hauer, J., Auer, F.
JAK2 p.G571S in B-cell precursor acute lymphoblastic leukemia: A synergizing germline susceptibility.
Leukemia 2019, DOI: 10.1038/s41375-019-0459-z. [PDF]
180. Klinker, S., Stindt, S., Gremer, L., Bode, J.G., Gertzen, C.G.W., Gohlke, H., Weiergräber, O.H., Hoffmann, S., Willbold, D.
Phosphorylated tyrosine 93 of hepatitis C virus nonstructural protein 5A is essential for interaction with host c-Src and efficient viral replication.
J. Biol. Chem. 2019, DOI: 10.1074/jbc.RA119.007656.
179. Bleffert, F., Granzin, J., Gohlke, H., Batra-Safferling, R., Jaeger, K.-E., Kovacic, F.
Expression, purification and crystallization of Pseudomonas aeruginosa esterase PA2949, a bacterial homologue of human membrane esterase ABHD6.
Acta Cryst. F 2019, 75, 270-277. [PDF]
178. Moussa, M., Ebrahima, W., Bonus, M., Gohlke, H., Mándi, A., Kurtán, T., Hartmann, R., Kalscheuer, R., Lin, W., Liu, Z., Proksch, P.
Co-culture of the fungus Fusarium tricinctum with Streptomyces lividans induces production of cryptic naphtoquinone dimers.
RSC Adv. 2019, 9, 1491–1500. [PDF]
177. Dreyer, I., Spitz, O., Kanonenberg, K., Montag, K., Handrich, M., Ahmad, S., Schott-Verdugo, S., Navarro-Retamal, C., Rubio-Meléndez, M., Gomez-Porras, J.L., Riedelsberger, J., Molina-Montenegro, M., Succurro, A., Zuccaro, A., Gould, S., Bauer, P., Schmitt, L., Gohlke, H.
Nutrient exchange in arbuscular mycorrhizal symbiosis from a thermodynamic point of view.
New Phytol. 2019, 222, 1043–1053. [PDF]
176. Dittrich, J., Schmidt, D., Pfleger, C., Gohlke, H.
Converging a knowledge-based scoring function: DrugScore2018.
J. Chem. Inf. Model. 2019, 59, 509-521. [PDF]
JCIM_2019
175. Reßing, N., Marquardt, V., Gertzen, C.G.W., Schöler, A., Schramm, A., Kurz, T., Gohlke, H., Aigner, A., Remke, M., Hansen, F.K.
Design, synthesis and biological evaluation of beta-peptoid-capped HDAC inhibitors with anti-neuroblastoma and anti-glioblastoma activity.
Med. Chem. Commun. 2019, DOI: 10.1039/C8MD00454D. [PDF]
174. Tanabe, K., Bonus, M., Tomiyama, S., Miyoshi, K., Nagi, M., Niimi, K., Chindamporn, A., Gohlke, H., Schmitt, L., Cannon, R., Niimi, M., Lamping, E.
FK506 resistance of Saccharomyces cerevisiae Pdr5 and Candida albicans Cdr1 involves mutations in the transmembrane domains and extracellular loops.
Antimicrob. Agents Chemother. 2019, 63, 1, e01146-18. [PDF]

2018

173.

Sanabria, H., Rodnin, D., Hemmen, K., Peulen, T.O., Felekyan, S., Fleissner, M.A., Dimura, M., Koberling, F., Kühnemuth, R., Hubbell, W.L., Gohlke, H., Seidel, C.A.M.
Resolving dynamics and function of transient states in single enzyme molecules.
arXiv:1812.06937 2018.
172. Mulnaes, D., Gohlke, H.
TopScore: Using deep neural networks and large diverse datasets for accurate protein model quality assessment.
J. Chem. Theory Comput. 2018, 14, 6117-6126. [PDF]
JCTC_2018

171.

Otte, M., Schweinitz, A., Bonus, M., Enke, U., Schumann, C., Gohlke, H., Benndorf, K.
Hydrophobic alkyl chains substituted to the 8-position of cyclic nucleotides enhance activation of CNG and HCN channels by an intricate enthalpy-entropy compensation.
Sci. Rep. 2018, 8, 14960. [PDF]
170. Kaletsch, A., Pinkerneil, M., Hoffmann, M.J., Vasudevan, A.A.J., Wang, C., Hansen, F.K., Wiek, C., Hanenberg, H., Gertzen, C.G.W., Gohlke, H., Kassack, M.U., Kurz, T., Schulz, W.A., Niegisch, G.
Effects of novel HDAC inhibitors on urothelial carcinoma cells.
Clin. Epigenetics 2018, 10, 100. [PDF]
169. Donner, L., Gremer, L., Ziehm, T., Gertzen, C.G.W., Gohlke, H., Willbold, D., Elvers, M.
Relevance of N-terminal residues for amyloid-β binding to platelet integrin αIIbβ3, integrin outside-in signaling and amyloid-β fibril formation.
Cell. Signal. 2018, 50, 121-130. [PDF]
168. Sueck, F., Poór, M., Faisal, Z., Gertzen, C.W.G., Cramer, B., Lemli, B., Kunsági-Máté, S., Gohlke, H., Humpf, H.-U.
Interaction of ochratoxin A and its thermal degradation product 2’R-ochratoxin A with human serum albumin.
Toxins 2018, 10, 256. [PDF]
167. Bhatia, S., Diedrich, D., Frieg, B., Ahlert, H., Stein, S., Bopp, B., Lang, F., Zang, T., Kroeger, T., Ernst, T., Kögler, G., Krieg, A., Lüdeke, S., Kunkel, H., Rodrigues Moita, A.J., Kassack, M.U., Marquardt, V., Opitz, F.V., Oldenburg, M., Remke, M., Babor, F., Grez, M., Hochhaus, A., Borkhardt, A., Groth, G., Nagel-Steger, L., Jose, J., Kurz, T., Gohlke, H., Hansen, F.K., Hauer, J.
Targeting HSP90 dimerization via the C terminus is effective in imatinib-resistant CML and lacks the heat shock response.
Blood 2018, 132, 3. [PDF] [Related Commentary]
166. Pagani, G., Gohlke, H.
On the contributing role of the transmembrane domain for subunit-specific sensitivity of integrin activation.
Sci. Rep. 2018, 8, 5733. [PDF]
165. Diederich, L., Suvorava, T., Sansone, R., Keller, T.C.S.K. IV, Barbarino, F., Sutton, T.R., Kramer, C.M., Lückstädt, W., Isakson, B.E., Gohlke, H., Feelisch, M., Kelm, M., Cortese-Krott, M.M.
On the effects of reactive oxygen species and nitric oxide on red blood cell deformability.
Front. Physiol. 2018, 9, 332. [PDF]
164. Wallot-Hieke, N., Verma, N., Schlütermann, D., Berleth, N., Deitersen, J., Böhler, P., Stuhldreier, F., Wu, W., Seggewiß, S., Peter, C., Gohlke, H., Mizushima, N., Stork, B.
Systematic analysis of ATG13 domain requirements for autophagy induction.
Autophagy 2018, 14, 5, 743-763. [PDF]
163. Milić, D., Dick, M., Mulnaes, D., Pfleger, C., Kinnen, A., Gohlke, H., Groth, G.
Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1.
Sci. Rep. 2018, 8, 3890. [PDF]
162. Pagani, G., Pereira, J.P.V., Stoldt, V.R., Beck, A., Scharf, R.E., Gohlke, H.
The human platelet antigen-1b (Pro33) variant of αIIbβ3 allosterically shifts the dynamic conformational equilibrium of this integrin toward the active state.
J. Biol. Chem. 2018, 293, 4830-4844. [PDF]
161. Rehberg, N., Akone, H.S., Ioerger, T.R., Erlenkamp, G., Daletos, G., Gohlke, H., Proksch, P., Kalscheuer, R.
Chlorflavonin targets acetohydroxyacid synthase catalytic subunit IlvB1 for synergistic killing of Mycobacterium tuberculosis.
ACS Infect. Dis. 2018, 4, 123-134. [PDF]
 
160. Gertzen, C.G.W., Keitel, V., Seidel, C.A.M., Gohlke, H.
Unravelling the di- and oligomerization interfaces of the G-protein coupled bile acid receptor TGR5 via integrative modeling.
"Proceedings of the NIC Symposium 2018", Binder, K., Müller, M., Trautmann, A. (eds.), Jülich, 2018, 25-31. [PDF]
159. Gu, Q., Zhang, Z., Gertzen, C.G.W., Häussinger, D., Gohlke, H., Münk, C.
Identification of a conserved interface of Human Immunodeficiency Virus Type 1 and Feline Immunodeficiency Virus Vifs with Cullin 5.
J. Virol. 2018, 92, 6. [PDF]

2017

158.

Pfleger, C., Minges, A., Boehm, M., McClendon, C.L., Torella, R., Gohlke, H.
Ensemble- and rigidity theory-based perturbation approach to analyze dynamic allostery.
J. Chem. Theory Comput. 2017, 13, 6343-6357. [PDF]
JCTC_2017
157. Yogesha, M., Venkatramanan, G.R., Martis, E.A.F., Coutinho, E.C., Gohlke, H., Chidangil, S., Dongre, P.M., D'Souza, J.S.
Structural features of FAP174, a MYCBP-1 orthologue from Chlamydomonas reinhardtii, revealed by computational and experimental analyses.
RSC Adv. 2017, 7, 51391–51402. [PDF]
156. Hanke, C.A., Gohlke, H.
Tertiary interactions in the unbound guanine-sensing riboswitch focus functional conformational variability on the binding site.
J. Chem. Inf. Model. 2017, 57, 2822-2832. [PDF]
155. 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. [PDF]
154. 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, 591, 3369–3377. [PDF]
153. Dröge, C., Bonus, M., Baumann, U., Klindt, C., Lainka, E., Kathemann, S., Brinkert, F., Grabhorn, E., Pfister, E.-D., 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 a large cohort of patients with cholestasis revealed a high number of different genetic variants.
J. Hepatol. 2017, 67, 1253–1264. [PDF]
152. Ciupka, D., Gohlke, H.
On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase.
Sci. Rep. 2017, 7, 8020. [PDF]
151. Bonus, M., Eichler, I., Gohlke, H.
Lipid transport by the ABC transporter MDR3.
Inside 2017, 15, 82-86.
150. Stenzel, K., Hamacher, A., Hansen, F.K., Gertzen, C.G.W., Senger, J., Marquardt, V., Marek, L., Marek, M., Romier, C., Remke, M., Jung, M., Gohlke, H., Kassack, U.M., Kurz, T.
Alkoxyurea-based histone deacetylase inhibitors increase cisplatin potency in chemoresistant cancer cell lines.
J. Med. Chem. 2017, 60, 5334-5348. [PDF]
149. Krieger, V., Hamacher, A., Gertzen, C.G.W., Senger, J., Zwindermann, M.R.H., Marek, M., Romier, C., Dekker, F.J., Kurz, T., Jung, M., Gohlke, H., Kassack, U.M., Hansen, F.K.
Design, multicomponent synthesis, and anticancer activity of a focused histone deacetylase (HDAC) inhibitor library with peptoid-based cap groups.
J. Med. Chem. 2017, 60, 5493-5506. [PDF]
148. 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]
147. 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. [PDF]
146. Gohlke, H., Ben-Shalom, I.Y., Kopitz, H., Pfeiffer-Marek, S., Baringhaus, K.-H.
Rigidity theory-based approximation of vibrational entropy changes upon binding to biomolecules.
J. Chem. Theory Comput. 2017, 13, 1495–1502. [PDF]
145. Minges, A, 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]
144. Hermans, S.M.A., Pfleger, C., Nutschel, C., Hanke, C.A., Gohlke, H.
Rigidity theory for biomolecules: Concepts, software, and applications.
WIREs Comput. Mol. Sci. 2017, 7, e1311. [PDF]
WIRES2017
143. Schanda, J., Lee, C.-W., Wohlan, K., Müller-Kuller, U., Kunkel, H., Quagliano-Lo Coco, I., Stein, S., Metz, A., Koch, J., Lausen, J., Medyouf, H., Gohlke, H., Heuser, M., Eder, M., Grez, M., Scherr, M., Wichmann, C.
Suppression of RUNX1/ETO oncogenic activity by a small molecule inhibitor of tetramerization.
Haematologica 2017, 102, e170-e174. [PDF]
142. Krieger, V., Ciglia, E, Thoma, R., Vasylyeva, V., Frieg, B., de Sousa Amadeu,, N., Kurz, T., Janiak, C., Gohlke, H., Hansen, F.K.
α-Aminoxy peptoids: A unique peptoid backbone with a preference for cis-amide bonds.
Chem. Eur. J. 2017, 23, 3699-3707. [PDF] Highlighted in Angew. Chemie
141. Ben-Shalom, I.Y., Pfeiffer-Marek, S., Baringhaus, K.-H., Gohlke, H.
Efficient approximation of ligand rotational and translational entropy changes upon binding for use in MM-PBSA calculations.
J. Chem. Inf. Model. 2017, 57, 170–189. [PDF]
140. Ghosh, S., Hönscheid, A., Dückers, G., Ginzel, S., Gohlke, H., Gombert, M., Kempkes, B., Klapper, W., Kuhlen, M., Laws, H.-J., Linka, R.M., Meisel, R., Mielke, C., Niehues, T., Schindler, D., Schneider, D., Schuster, F.R., Speckmann, C., Borkhardt, A.
Human RAD52 – a novel player in DNA repair in cancer and immunodeficiency.
Haematologica 2017, 102, e69-e72. [PDF]

2016


139. Dimura, M., Peulen, T.O., Hanke, C.A., Prakash, A., Gohlke, H., Seidel, C.A.M.
Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems.
Curr. Opin. Struct. Biol. 2016, 40, 163–185. [PDF]
     
138. 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. [PDF]
   
137. Spiegel, J.D., Fulle, S., Kleinschmidt, M., Gohlke, H., Marian, C.M.
Failure of the IDA in FRET systems at close inter-dye distances is moderated by frequent low κ2 values.
J. Phys. Chem. B 2016, 120, 8845–8862. [PDF]
     
136. Diedrich, D., Rodrigues Moita, A.J., Rüther, A., Frieg, B., Reiss, G.J., Hoeppner, A., Kurz, T., Gohlke, H., Lüdeke, S., Kassack, M.U., Hansen, F.K.
α-Aminoxy oligopeptides: synthesis, secondary structure and cytotoxicity of a novel class of anticancer foldamers.
Chem. Eur. J. 2016, 22, 17600–17611. [PDF]
     
135. Zhang, Z., Gu, Q., Vasudevan, A.A.J., Hain, A., Kloke, B.-P., Hasheminasab, S., Mulnaes D., Sato, K., Cichutek, K., Häussinger, D., Bravo, I.G., Smits, S.H.J., Gohlke, H., Münk, C.
Determinants of FIV and HIV Vif sensitivity of feline APOBEC3 restriction factors.
Retrovirology 2016, 13, 46. [PDF]
     
134. Nguyen, G.T.T., Erlenkamp, G., Jäck, O., Küberl, A., Bott, M., Fiorani, F., Gohlke, H., Groth, G.
Chalcone-based selective inhibitors of a C4 plant key enzyme as novel potential herbicides.
Sci. Rep. 2016, 6, 27333. [PDF]
   
133. Bisterfeld, C., Classen, T., Küberl, I., Henßen, B., Metz, A., Gohlke, H., Pietruszka, J.
Redesigning aldolase stereoselectivity by homologous grafting.
PLOS ONE 2016, 11, e0156525. [PDF]
   
132. 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.
Platelets contribute to amyloid-β aggregation in cerebral vessels through integrin αIIbβ3-induced outside-in signaling and clusterin release.
Sci. Signal. 2016, 9, RA52. [PDF] [Related Commentary]
   
131. Ioannidis, H., Drakopoulos, A., Tzitzoglaki, C., Homeyer, N., Kolarov, F., Gueka, P., Freudenberger, K., Liolios, C., Gauglitz, G., Cournia, Z., Gohlke, H., Kolocouris, A.
Alchemical free energy calculations and isothermal titration calorimetry measurements of aminoadamantanes bound to the closed state of influenza A/M2TM.
J. Chem. Inf. Model. 2016, 56, 862–876. [PDF]
   
130. Khosa, S., Hoeppner, A., Gohlke, H., Schmitt, L., Smits, S.H.J.
Structure of the response regulator NsrR from Streptococcus agalactiae, which is involved in lantibiotic resistance.
PLOS ONE 2016, 11, e0149903. [PDF]
   
129. Rathi, P.C., Fulton, A., Jaeger, K.-E., Gohlke, H.
Application of rigidity theory to the thermostabilization of lipase A from Bacillus subtilis.
PLOS Comp. Biol. 2016, 12, e1004754. [PDF]
   
128. Diedrich, D., Hamacher, A., Gertzen, C.G.W., Alves Avelar, L.A., Reiss, G.J., Kurz, T., Gohlke, H., Kassack, M.U., Hansen, F.K.
Rational design and diversity-oriented synthesis of peptoid-based selective HDAC6 inhibitors.
Chem. Commun. 2016, 52, 3219-3222. [PDF]
   
127. Bopp, B., Ciglia, E., Ouald-Chaib, A., Groth, G., Gohlke, H., Jose, J.
Design and biological testing of peptidic dimerization inhibitors of human Hsp90 that target the C-terminal domain.
BBA - Gen. Subjects 2016, 1860, 1043–1055. [PDF]
   
126. Homeyer, N., Ioannidis, H., Kolarov, F., Gauglitz, G., Zikos, C., Kolocouris, A., Gohlke, H.
Interpreting thermodynamic profiles of aminoadamantane compounds inhibiting the M2 proton channel of influenza A by free energy calculations.
J. Chem. Inf. Model. 2016, 56, 110-126. [PDF]
   
125. Dick, M., Weiergraeber, O.H., Classen, T., Bisterfeld, C., Bramski, J., Gohlke, H., Pietruszka, J.
Trading off stability against activity in extremophilic aldolases.
Sci. Rep. 2016, 6, 17908. [PDF]
 
124. Khosa, S., Frieg, B., Mulnaes, D., Kleinschrodt, D., Hoeppner, A., Gohlke, H., Smits, S.H.J.
Structural basis of lantibiotic recognition by the nisin resistance protein from Streptococcus agalactiae.
Sci. Rep. 2016, 6, 18679. [PDF]
   
123. 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. [PDF]
   
122. Frieg, B., Häussinger, D., Gohlke, H.
Towards restoring catalytic activity of glutamine synthetase with a clinically relevant mutation.
in:"Proceedings of the NIC Symposium 2016", Binder, K., Müller, M., Kremer, M., Schnurpfeil, A. (eds.), Jülich, 2016, 97-104. [PDF]
   
121. Dixit, V.A., Rathi, P.C., S. Bhagat, Gohlke, H., Petersen, R.K., Kristiansen, K., Chakraborti, A.K., Bharatam, P.V.
Design and synthesis of novel Y-shaped barbituric acid derivatives as PPARγ activators.
Eur. J. Med. Chem. 2016, 108, 423-435. [PDF]
   

2015


120. Gertzen, C.G.W., Spomer, L., Smits, S.H.J., Häussinger, D., Keitel, V., Gohlke, H.
Mutational mapping of the transmembrane binding site of the G-Protein coupled receptor TGR5 and binding mode prediction of TGR5 agonists.
Eur. J. Med. Chem. 2015, 104, 57-72. [PDF]
   
119. 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. [PDF]
NAR_2015
118. Alchab, F., Ettouati, L., Bouaziz, Z., Bollacke, A., Delcros, J.-G., Gertzen, C.G.W., Gohlke, H., Pinaud, N., Marchivie, M., Guillon, J., Fenet, B., Jose, J., Le Borgne, M.
Synthesis, biological evaluation, and molecular modeling of substituted indeno[1,2-b]indoles as inhibitors of human protein kinase CK2.
Pharmaceuticals 2015, 279-302. [PDF]
 
117. Rathi, P.C., Jaeger, K.-E., Gohlke, H.
Structural rigidity and protein thermostability in variants of lipase A from Bacillus subtilis.
PLOS ONE 2015, 10, e0130289. [PDF]
   
116. Rathi, P.C., Mulnaes, D., Gohlke, H.
VisualCNA: a GUI for interactive Constraint Network Analysis and protein engineering for improving thermostability.
Bioinformatics 2015, 31, 2394–2396. [PDF]
 
115. Herkommer, D., Dreisigacker, S., Sergeev, G., Sasse, F., Gohlke, H., Menche, D.
Design, synthesis and biological evaluation of simplified side chain hybrids of the potent actin binding polyketides rhizopodin and bistramide.
ChemMedChem 2015, 10, 470-489. [PDF]
   
114. Homeyer, N., Gohlke, H.
Extension of the free energy workflow FEW towards implicit solvent / implicit membrane MM-PBSA calculations.
BBA - Gen. Subjects 2015, 1850, 972–982. [PDF]
   
113. 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. [PDF]
   

2014


112. Frieg, B., Homeyer, N., Gohlke, H.
Glutamine synthetase mutations that cause glutamine deficiency: mechanistic insights from molecular dynamics simulations.
Eur. J. Med. Res. 2014, 19(Suppl 1), S15. [PDF]
   
111. Bonus, M., Sommerfeld, A., Häussinger, D., Gohlke, H.
α5β1 integrins in hepatocytes act as receptors for bile acids with a (nor)ursodeoxycholane scaffold.
Eur. J. Med. Res. 2014, 19(Suppl 1), S13. [PDF]
   
110. Koch, A., Ma, Q., Frohnapfel, M., Spomer, L., Keitel, V., Gertzen, C.G.W., Gohlke, H., Seidel, C.A.M.
High-precision FRET analysis of the G-protein coupled receptor TGR5 in live cells.
Eur. J. Med. Res. 2014, 19(Suppl 1), S12. [PDF]
   
109. Gertzen, C.G.W.,Spomer, L., Schmitz, B., Häussinger, D., Keitel, V., Gohlke, H.
The secondary structure of the TGR5 membrane-proximal C-terminus determines plasma membrane localization and responsiveness towards extracellular ligands.
Eur. J. Med. Res. 2014, 19(Suppl 1), S14. [PDF]
   
108. Homeyer, N., Stoll, F., Hillisch, A., Gohlke, H.
Binding free energy calculations for lead optimization: Assessment of their accuracy in an industrial drug design context.
J. Chem. Theory Comput. 2014, 10, 3331−3344. [PDF]   Access the recommendation on F1000 Prime
JCTC_8_2014
107.

Krüger, D.M., Ignacio Garzon, J., Chacon, P., Gohlke, H.
DrugScore^PPI knowledge-based potentials used as scoring and objective function in protein-protein docking.
PLOS ONE 2014, 9, e89466. [PDF]

   
107. Krüger, D.M., Ignacio Garzon, J., Chacon, P., Gohlke, H.
DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking.
PLOS ONE 2014, 9, e89466. [PDF]
   
106. Rathi, P.C., Hoeffken, H.W., Gohlke, H.
Quality matters: Extension of clusters of residues with good hydrophobic contacts stabilize (hyper)thermophilic proteins.
J. Chem. Inf. Model. 2014, 54, 355–361. [PDF]
   
105. Hanke, C.A., Gohlke, H.
How tertiary interactions between the L2 and L3 loops affect the dynamics of the distant ligand binding site in the guanine sensing riboswitch.
in:"Proceedings of the NIC Symposium 2014", Binder, K., Münster, G., Kremer, M. (eds.), Jülich, 2014, 99-106. [PDF]
   
104. Ciglia, E., Vergin, J., Reimann, S., Smits, S.H.J., Schmitt, L., Groth, G., Gohlke, H.
Resolving hot spots in the C-terminal dimerization domain that determine the stability of the molecular chaperone Hsp90.
PLOS ONE 2014, 9, e96031. [PDF]
   
103. Spomer, L., Gertzen, C.G.W., Schmitz, B., Häussinger, D., Gohlke, H., Keitel, V.
A membrane-proximal, C-terminal α-helix is required for plasma membrane localization and function of the G Protein-Coupled Receptor (GPCR) TGR5.
J. Biol. Chem. 2014, 289, 3689-3702. [PDF]
   
102. Spanier, L., Ciglia, E., Hansen, F.K., Kuna, K., Frank, W., Gohlke, H., Kurz, T.
Design, synthesis, and conformational analysis of trispyrimidonamides as α-helix mimetics.
J. Org. Chem. 2014, 79, 1582–1593. [PDF]
   
101. Metz, A., Ciglia, E., Kröger, T., Gohlke, H.
Protein-Protein-Interaktionen nachgeahmt: Strukturbasierte Identifizierung niedermolekularer Inhibitoren.
GIT - Labor-Fachzeitschrift 2014, 8, 33-35. [PDF]
   
100. Widderich, N., Pittelkow, M., Höppner, A., Mulnaes, D., Buckel, W., Gohlke, H., Smits, S.H.J., Bremer, E.
Molecular dynamics simulations and structure-guided mutagenesis provide insight into the architecture of the catalytic core of the ectoine hydroxylase.
J. Mol. Biol. 2014, 426, 586-600. [PDF]
   

2013


99. Gohlke, H., Hergert, U., Meyer, T., Mulnaes, D., Grieshaber, M.K., Smits, S.H.J., Schmitt, L.
Binding region of alanopine dehydrogenase predicted by unbiased molecular dynamics simulations of ligand diffusion.
J. Chem. Inf. Model. 2013, 53, 2493–2498. [PDF] Access the recommendation on F1000 Prime
   
98. 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. [PDF]
   
97. Metz, A., Schanda, J., Grez, M., Wichmann, C., Gohlke, H.
From determinants of RUNX1/ETO tetramerization to small-molecule protein-protein interaction inhibitors targeting acute myeloid leukemia.
J. Chem. Inf. Model. 2013, 53, 2197-2202. [PDF]
   
96. Pfleger, C., Gohlke, H.
Efficient and Robust Analysis of Biomacromolecular Flexibility Using Ensembles of Network Topologies Based on Fuzzy Noncovalent Constraints.
Structure 2013, 21, 1725–1734. [PDF]
Structure2013  
95. Krüger, D.M., Gohlke, H.
Proteinstabilität webbasiert analysieren.
Nachrichten aus der Chemie 2013, 61, 909–911. [PDF]
   
94. Krüger, D.M., Rathi, P.C., Pfleger, C., Gohlke, H.
CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function.
Nucleic Acids Res. 2013, 41, W340-348. [PDF]
   
93. Pfleger, C., Rathi, P.C., Klein, D., Radestock, S., Gohlke, H.
Constraint Network Analysis (CNA): A python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function.
J. Chem. Inf. Model. 2013, 53, 1007-1015. [PDF]
JCIM_04_2013
92. Urban, C., Hamacher, A., Partke, H.-J., Roden, M., Schinner, S., Christiansen, E., Due-Hansen, M.E., Ulven, T., Gohlke, H., Kassack, M.
In vitro and mouse in vivo characterization of the potent free fatty acid 1 receptor agonist TUG-469.
N.-S. Arch. Pharmacol. 2013, 386, 1021-1030. [PDF]
   
91. Homeyer, N., Gohlke, H.
Advances in molecular dynamics simulations and free energy calculations relevant for drug design.
in: "In silico drug discovery and design techniques" , M. Lill (ed.), 2013. [PDF]
 
90. Gohlke, H., Schmitz, B., Sommerfeld, A., Reinehr, R., Häussinger, D.
α5ß1-Integrins act as long-searched tauroursodeoxycholic acid receptors in hepatocytes.
in: "XXII International Bile Acid Meeting – Hepatic and Extrahepatic Targets of Bile Acid Signaling. Falk Symposium 184, Vienna, 2012", D. Häussinger (ed.), 2013, 59-62.
 
89. Gohlke, H., Schmitz, B., Sommerfeld, A., Reinehr, R., Häussinger, D.
α5ß1-Integrins are sensors for tauroursodeoxycholic acid in hepatocytes.
Hepatology 2013, 57, 1117–1129. [PDF] [Editorial] Access the recommendation on F1000 Prime
HEPTOLOGY_03_2013
88. Arslan, Z., Wurm, R., Brener, O., Ellinger, P., Nagel-Steger, L., Oesterhelt, F., Schmitt, L., Willbold, D., Wagner, R., Gohlke, H., Smits, S.H.J., Pul, Ü.
Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2.
Nucleic Acids Res. 2013, 41, 6347-6359. [PDF]
   
87. Marek, L., Hamacher, A., Hansen, F., Kuna, K., Gohlke, H., Kassack, M., Kurz, T.
HDAC-inhibitors with a novel connecting unit linker region reveal a seelectivity profile for HDAC4 and HDAC5 with improved activity against chemoresistant cancer cells.
J. Med. Chem. 2013, 56, 427–436. [PDF]
   
86. Pfleger, C., Radestock, S., Schmidt, E., Gohlke, H.
Global and local indices for characterizing biomolecular flexibility and rigidity.
J. Comput. Chem. 2013, 34, 220-233. [PDF]
JCC_04_2013
85. Homeyer, N., Gohlke, H.
FEW - A workflow tool for free energy calculations of ligand binding.
J. Comput. Chem. 2013, 34, 965–973. [PDF]
   

2012


84. Krüger, D.M., Jessen, G., Gohlke, H.
How good are state-of-the-art docking tools in predicting ligand binding modes in protein-protein interfaces?
J. Chem. Inf. Model. 2012, 52, 2807-2811. [PDF]
 
83. Krüger, D.M., Gohlke, H.
Proteindynamik webbasiert analysieren.
Nachrichten aus der Chemie 2012, 60, 1010-1012. [PDF]
 
82. Gohlke, H., Schlieper, D., Groth, G.
Resolving the negative potential side (n-side) water-accessible proton pathway of F-type ATP synthase by molecular dynamics simulations.
J. Biol. Chem. 2012, 287, 36536-36543. [PDF]
 
81. Miller, B.R., McGee, T.D., Swails, J.M., Homeyer, N., Gohlke, H., Roitberg, A.E.
MMPBSA.py: An Efficient program for end-state free energy calculations.
J. Chem. Theory Comput. 2012, 8, 3314–3321. [PDF]
 
80. Nisius, B., Gohlke, H.
Alignment-independent comparison of binding sites based on DrugScore potential fields encoded by 3D Zernike descriptors.
J. Chem. Inf. Model. 2012, 52, 2339–2347. [PDF]
 
79. Dreisigacker, S., Latek, D., Bockelmann, S., Huss, M., Wieczorek, H., Filipek, S., Gohlke, H., Menche, D., Carlomagno, T.
Understanding the inhibitory effect of highly potent and selective Archazolides binding to the vacuolar ATPase.
J. Chem. Inf. Model. 2012, 52, 2265–2272. [PDF]
 
78. Kalinin, S., Peulen, T., Sindbert, S., Rothwell, P.J., Berger, S., Restle, T., Goody, R.S., Gohlke, H., Seidel, C.A.M.
A toolkit and benchmark study for FRET-restrained high-precision structural modeling.
Nature Methods 2012, 9, 1218–1225. [PDF] [Related commentary] Access the recommendation on F1000 Prime
NAT_METHODS_9_2012
77. Pinto Gomes, C., Metz, A., Bats, J.W., Gohlke, H., Goebel, M.W.
Modular solid-phase synthesis of Teroxazoles as a class of α-helix mimetics.
Eur. J. Org. Chem., 2012, 3270-3277. [PDF]
 
76. Gertzen, C.G.W., Gohlke, H.
From Hansch-Fujita analysis to AFMoC: A road to structure-based QSAR.
Molecular Informatics 2012, 31, 698–704. [PDF]
 
75. Krüger, D.M., Ahmed, A., Gohlke, H.
NMSim webserver: Integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins.
Nucleic Acids Res. 2012, 40, W310-W316. [PDF]
 
74. Fulle, S., Gohlke, H.
Flexibility analysis of biomacromolecules with application to computer-aided drug design.
in: "Methods in Molecular Biology - Computational Drug Discovery and Design", R. Baron (ed.), 2012, 819, 75-91. [PDF]
 
73. Metz, A., Pfleger, C., Kopitz, H., Pfeiffer-Marek, S., Baringhaus, K.-H., Gohlke, H.
Hot spots and transient pockets: Predicting the determinants of small-molecule binding to a protein-protein interface.
J. Chem. Inf. Model. 2012, 52, 120-133. [PDF] Highlighted in JCIM/JMC virtual issue on "Computational Methods for Drug Discovery and Design".
 
72. Ellinger, P., Arslan, Z., Wurm, R., Tschapek, B., MacKenzie, C., Pfeffer, K., Panjikar, S., Wagner, R., Schmitt, L., Gohlke, H., Pul, U., Smits, S.H.J.
The crystal structure of the CRISPR-associated protein Csn2 from Streptococcus agalactiae.
J. Struct. Biol. 2012, 178, 350-362. [PDF]
 
71. Metz, A., Ciglia, E., Gohlke, H.
Modulating protein-protein interactions: From structural determinants of binding to druggability prediction to application.
Curr. Pharm. Des. 2012, 18, 4630-4647. [PDF]
 
70. Kopitz, H., Cashman, D.A., Pfeiffer-Marek, S., Gohlke, H.
Influence of the solvent representation on vibrational entropy calculations: Generalized Born versus Distance-Dependent Dielectric Model.
J. Comput. Chem. 2012, 33, 1004–1013. [PDF]
 
69. Homeyer, N., Gohlke, H.
Free energy calculations by the molecular mechanics Poisson−Boltzmann surface area method.
Molecular Informatics 2012, 31, 114–122. [PDF]
 
68. Nisius, B., Sha, F., Gohlke, H.
Structure-based computational analysis of protein binding sites for function and druggability prediction.
J. Biotechnol. 2012, 159, 123-134. [PDF]
 
67. Rathi, P.C., Radestock, S., Gohlke, H.
Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio.
J. Biotechnol. 2012, 159, 135-144. [PDF]
 
66. Grimme, D., Gonzalez-Ruiz, D., Gohlke, H.
Computational strategies and challenges for targeting protein-protein interactions with small molecules.
in: RSC Drug Discovery Series No. 23, "Physico-chemical and Computational Approaches to Drug Discovery", F.J. Luque, X. Barril (eds.),2012, 319-359. [PDF]
 
65. Gohlke, H., Bozilovic, J., Engels, J.W.
Synthesis and properties of fluorinated nucleobases in DNA and RNA.
in: "Fluorine in Pharmaceutical and Medicinal Chemistry: From Biophysical Aspects to Clinical Applications", V. Gouverneur, K. Mueller (eds.), London 2012, 3-32. [PDF]
 

2011


64. Klein, D.L., Hao, J., Berry, A., Gohlke, H.
Influence of thermostabilizing mutations in fructose-1,6-bisphosphate aldolases revealed by constraint network analysis.
in: "From Computational Biophysics to Systems Biology (CBSB11)", P. Carloni, U.H.E. Hansmann, T. Lippert, J. H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann (eds.), IAS Series, Jülich, 2011, 8, 71-74.
 
63. Saini, J., Fulle, S., Gohlke, H.
Molecular dynamics simulations of ribosome-oxazolidinone complexes reveal structural aspects for antibiotics design.
in: "From Computational Biophysics to Systems Biology (CBSB11)" , P. Carloni, U.H.E. Hansmann, T. Lippert, J. H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann (eds.), IAS Series, Jülich, 2011, 8, 173-177. [PDF]
 
62. Krüger, D.M., Garzon, J. I., Chacon, P., Gohlke, H.
Predicting protein-protein interactions with DrugScorePPI: Docking, scoring, and in silico alanine-scanning.
in: "From Computational Biophysics to Systems Biology (CBSB11)" , P. Carloni, U.H.E. Hansmann, T. Lippert, J. H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann (eds.), IAS Series, Jülich, 2011, 8, 105-108. [PDF]
 
61. Tschapek, B., Pittelkow, M., Sohn-Bösser, L., Holtmann, G., Smits, S.H.J., Gohlke, H., Bremer, E., Schmitt, L.
Arg149 is involved in switching the low affinity, open state of the binding protein AfProX into its high affinity, closed state.
J. Mol. Biol. 2011, 411, 36-52. [PDF]
 
60. Craig, I., Pfleger, C., Gohlke, H., Essex, J.W., Spiegel, K.
Pocket-space maps to identify novel binding-site conformations in proteins.
J. Chem. Inf. Model. 2011, 51, 2666–2679. [Preprint]
JCIM_10_2011
59. Rathi, P.C., Pfleger, C., Fulle, S., Klein, D.L., Gohlke, H.
Statics of biomacromolecules.
in: "Modeling of Molecular Properties" , P. Comba (ed.), S. 281-299, Wiley-VCH, Weinheim, 2011. [PDF]
 
58. Klein, D.L., Radestock, S., Gohlke, H.
Analyzing protein rigidity for understanding and improving thermal adaptation.
in: "Thermostable Proteins: Structural Stability and Design" , S. Sen, L. Nilsson (eds.), S. 47-67, CRC Press Taylor & Francis Group, Boca Raton, 2011. [PDF]
 
57. Ahmed, A., Rippmann, F., Barnickel, G., Gohlke, H.
A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins.
J. Chem. Inf. Model. 2011, 51, 1604-1622. [PDF]
 
56. Krüger, D.M., Bergs, J., Kazemi, S., Gohlke, H.
Target flexibility in RNA-ligand docking modeled by elastic potential Grids.
ACS Med Chem Lett 2011, 2, 489-493. [PDF]
MED_CHEM_LET_2011
55. Krüger, D.M., Gohlke, H.
Protein-Protein-Interaktionen webbasiert analysieren.
Nachrichten aus der Chemie 2011, 59, 44-45. [PDF]
 
54. Radestock, S., Gohlke, H.
Protein rigidity and thermophilic adaptation.
Proteins 2011, 79, 1089-1108. [PDF]
 

2010


53. Gohlke, H.
Strukturbasierte Modellierung der molekularen Erkennung auf multiplen Skalen.
in: "Neues aus Wissenschaft und Lehre - Jahrbuch der Heinrich-Heine-Universitaet Duesseldorf 2010", H.M. Piper (ed.), 2010, 311-324. [PDF]
 
52. Ahmed, A., Villinger, S., Gohlke, H.
Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses.
Proteins 2010, 78, 3341–3352. [PDF]
 
51. Reinehr, R., Gohlke, H., Sommerfeld, A., vom Dahl, S., Häussinger, D.
Activation of integrins by urea in perfused rat liver.
J. Biol. Chem. 2010, 285, 29348-29356. [PDF]
 
50.

Fulle, S., Christ, N.A., Kestner, E., Gohlke, H.
HIV-1 TAR RNA spontaneously undergoes relevant Apo-to-Holo conformational transitions in molecular dynamics and constrained geometrical simulations.               
J. Chem. Inf. Model. 2010, 50, 1489–1501. [PDF]

JCIM_8_2010
49. Krüger, D.M., Gohlke, H.
DrugScore^PPII webserver: Fast and accurate in silico alanine scanning for scoring protein-protein interactions.
Nucleic Acids Res. 2010, 38, W480-W486. [PDF]
 
48. Gohlke, H., Kopitz, H.
Protein flexibility in in silico screening.
in: "Burger's Medicinal Chemistry, Drug Discovery, and Development, 7th Edition", D.J. Abraham, D.P. Rotella (eds.), 2010, 867-887. [PDF]
 
47. Wichmann, C., Becker, Y., Chen-Wichmann, L., Vogel, V., Vojtkova, A., Herglotz, J., Moore, S., Koch, J., Lausen, J., Mäntele, W., Gohlke, H., Grez, M.
Dimer-tetramer transition controls RUNX1/ETO leukemogenic activity.
Blood 2010, 116, 603-613. [PDF]
 
46. Koller, A.N., Bozilovic, J., Engels, J.W., Gohlke, H.
Aromatic N versus aromatic F: bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs.
Nucleic Acids Res. 2010, 38, 3133-3146. [PDF]
 
45. Fulle, S., Gohlke, H.
Molecular recognition of RNA: Challenges for modelling interactions and plasticity.
J. Mol. Recognit. 2010, 23, 220-231. [PDF]
 

2009


44. Gonzalez-Ruiz, D., Gohlke, H.
Steering protein-ligand docking with quantitative NMR chemical shift perturbations.
J. Chem. Inf. Model. 2009, 49, 2260-2271. [PDF]
 
43. Ahmed, A., Gohlke, H.
Multi-scale modeling of macromolecular conformational changes.
in: "Proceedings of the 1st International Conference on Computational & Mathematical Biomedical Engineering (CMBE09)" ,
Nithiarasu, P., Löhner, R. (eds.), Swansea 2009, 219-222. [PDF]
 
42. Kazemi, S., Krüger, D.M., Sirockin, F., Gohlke, H.
Elastic potential grids: Accurate and efficient representation of intermolecular interactions for fully flexible docking.
ChemMedChem 2009, 4, 1264-1268. [PDF]
 
41. Fulle, S., Gohlke, H.
Constraint counting on RNA structures: Linking flexibility and function.
Methods 2009, 49, 181-188. [PDF]
 
40. Fulle, S., Gohlke, H.
Statics of the ribosomal exit tunnel: Implications for cotranslational peptide folding, elongation regulation, and antibiotics binding.
J. Mol. Biol. 2009, 387, 502-517. [PDF] [Suppl. Data]
 

2008


39. Radestock, S., Gohlke, H.
Constraint Network Analysis: Exploiting the link between protein rigidity and thermostability.
in: "From Computational Biophysics to Systems Biology (CBSB08)", U.H.E. Hansmann, J. H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann (eds.), NIC Series, Jülich 2008, 40, 357-360. [PDF]
 
38.
Fulle, S., Gohlke, H.
Determining RNA flexibility by graph theory: Ribosomal exit tunnel as a case study.
in: "From Computational Biophysics to Systems Biology (CBSB08)", U.H.E. Hansmann, J. H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann (eds.), NIC Series, Jülich 2008, 40, 213-216. [PDF]
 
37. Radestock, S., Gohlke, H.
Exploiting the link between protein rigidity and thermostability for data-driven protein engineering.
Eng. Life Science 2008, 8, 507-522. [PDF] [Corrigendum]
 
36. Kopitz, H., Zivkovic, A., Engels, J.W., Gohlke, H.
Determinants of the unexpected stability of RNA fluorobenzene self pairs.
ChemBioChem 2008, 9, 2619-2622. [PDF] [Suppl. Data]
 
35. Cozzini P., Kellogg G.E., Spyrakis, F., Abraham, D. J., Costantino, G., Emerson A., Fanelli, F., Gohlke, H., Kuhn, L.A., Morris, G.M., Orozco, M., Pertinhez, T. A., Rizzi, M., Sotriffer C.A.
Target flexibility: An emerging consideration in drug discovery and design.
J. Med. Chem. 2008, 51, 6237-6255. [PDF]
 
34. Koller, A.N., Schwalbe, H., Gohlke, H.
Starting structure dependence of NMR order parameters derived from MD simulations: Implications for judging force-field quality.
Biophys. J. 2008, 95, L4-L6. [PDF]
 
33. Fulle, S., Gohlke, H.
Analyzing the flexibility of RNA structures by constraint counting.
Biophys. J. 2008, 94, 4202-4219. [PDF] [Suppl. Data]
 
32. Wendel, C., Gohlke, H.
Predicting transmembrane helix pair configurations with knowledge-based distance-dependent pair potentials.
Proteins 2008, 70, 984-999. [PDF]
 

2007


31. Breu, B., Silber, K., Gohlke, H.
Consensus Adaptation of Fields for Molecular Comparison (AFMoC) models incorporate ligand and receptor conformational variability into tailor-made scoring functions.
J. Chem. Inf. Model. 2007, 47, 2383-2400. [PDF]
 
30. Pfeffer, P., Gohlke, H.
DrugScoreRNA-knowledge-based scoring function to predict RNA-ligand interactions.
J. Chem. Inf. Model. 2007, 47, 1868-1876. [PDF]
 
29. Radestock, S., Gohlke, H.
Molekulare Bioinformatik in der Pharmaforschung.
Bioforum 2007, 3, 50-52. [PDF]
 
28. Ahmed, A., Kazemi, S., Gohlke, H.
Protein flexibility and mobility in structure-based drug design.
Front. Drug Des. Discov. 2007, 3, 455-476. [PDF]
 
27. Rashid, U.J., Peternov, D., Koglin, A., Gohlke, H., Piehler, J., Chen, J.C.-H.
Structure of Aquifex aeolicus Argonaute highlights conformational flexibility of the PAZ domain as a potential regulator of RNA-induced silencing complex function.
J. Biol. Chem. 2007, 282, 13824-13832. [PDF]
 

2006


26. Gohlke, H., Thorpe, M.F.
A natural coarse graining for simulating large biomolecular motion.
Biophys. J. 2006, 91, 2115-2120. [PDF] Access the recommendation on F1000 Prime
 
25. Gonzalez-Ruiz, D., Gohlke, H.
Targeting protein-protein interactions with small molecules: Challenges and perspectives for computational binding epitope detection and ligand finding.
Curr. Med. Chem. 2006, 13, 2607-2625. [PDF]
 
24. Ahmed, A., Gohlke, H.
Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory.
Proteins 2006, 63, 1038-1051. [PDF]
 

2005


23. Velec, H.F.G. , Gohlke, H., Klebe, G.
DrugScoreCSD-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction.
J. Med. Chem. 2005, 48, 6296 - 6303. [PDF]
 
22. Radestock, S., Boehm, M., Gohlke, H.
Improving binding mode predictions by docking into protein-specifically adapted potential fields.
J. Med. Chem. 2005, 48, 5466 - 5479. [PDF]
 
21. Case, D.A., Thomas, E., Cheatham, T. , Darden, T., Gohlke, H., Luo, R., Merz, K.M., Onufriev, A., Simmerling, C., Wang, B., Woods, R.J.
The Amber biomolecular simulation programs.
J. Comp. Chem. 2005, 26, 1668-1688. [PDF]
 

2004


20. Ferrara, P., Gohlke, H., Price, D.J., Klebe, G., Brooks III, C.L.
Assessing scoring functions for protein-ligand interactions.
J. Med. Chem. 2004, 47, 3032-3047. [PDF]
 
19. Gohlke, H., Kuhn, L.A., Case, D.A.
Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach.
Proteins 2004, 56, 322-327. [PDF]
 
18. Gohlke, H., Case, D.A.
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.
J. Comput. Chem. 2004, 25, 238-250. [PDF] Access the recommendation on F1000 Prime
 

2003


17. Evers, A., Gohlke, H., Klebe, G.
Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials.
J. Mol. Biol. 2003, 334, 327-345. [PDF]
 
16. Gohlke, H., Kiel, C., Case, D.A.
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.
J. Mol. Biol. 2003, 330, 891-913. [PDF]
 
15. Gohlke, H., Schwarz, S., Gündisch, D., Tilotta, M.C., Weber, A., Wegge, T., Seitz, G.
3D-QSAR analyses-guided rational design of novel ligands for the central nicotinic acetylcholine receptor.
J. Med. Chem. 2003, 46, 2031-2048. [PDF]
 

2002


14. Gohlke, H., Klebe, G.
DrugScore meets CoMFA: Adaptation of Fields for Molecular Comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein.
J. Med. Chem. 2002, 45, 4153-4170. [PDF]
 
13a. Gohlke, H., Klebe, G.
Ansätze zur Beschreibung und Vorhersage der Bindungsaffinität niedermolekularer Liganden an makromolekulare Rezeptoren.
Angew. Chem. 2002, 114, 2764-2798. [PDF]
 
13. Gohlke, H., Klebe, G.
Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors.
Angew. Chem. Int. Ed. 2002, 41, 2644-2676. [PDF]
 
12. Sotriffer, C.A., Gohlke, H., Klebe, G.
Docking into knowledge-based potential fields: A comparative evaluation of DrugScore.
J. Med. Chem. 2002, 45, 1967-1970. [PDF]
 
11. Gohlke, H., Gündisch, D., Schwarz, S., Seitz, G., Tilotta, M.C., Wegge, T.
Synthesis and nicotinic binding studies on enatiopure Diazine analogues of the novel (2-Chloro-5-pyridyl)-9-azabicyclo[4.2.1]non-2-ene UB-165.
J. Med. Chem. 2002, 45, 1064-1072. [PDF]
 

2001


10. Kamm, W., Hauptmann, J., Behrens, I., Stürzebecher, J., Behrens, I., Dullweber, F., Gohlke, H., Stubbs, M., Klebe, G., Kissel, T.
Transport of peptidomimetic thrombin inhibitors with a 3-Amidino-Phenylalanine structure: Permeability and efflux mechanism in monolayers of a human intestinal cell line (Caco-2).
Pharm. Res. 2001, 18, 1110-1118. [PDF]
 
9. Gohlke, H., Klebe, G.
Scoring protein-ligand interactions: developments and applications in virtual screening.
Eur. J. Biochem. 2001, 268, Suppl. 1, 30.
 
8. Gohlke, H., Klebe, G.
Statistical potentials and scoring functions applied to protein-ligand binding.
Curr. Opin. Struct. Biol. 2001, 11, 231-235. (Invited review) [PDF]
 
7. Gohlke, H., Dullweber, F., Kamm, W., März, J., Kissel, T., Klebe, G.
Prediction of human intestinal absorption using a combined simulated annealing/backpropagation neural network approach.
In Rational Approaches to Drug Design - 13th European Symposium on QSAR (Höltje, H.-D., Sippl, W., Ed.), S. 261-271, Prous Science, Barcelona, 2001.
 

2000


6. Gohlke, H., Hendlich M., Klebe G.
Predicting binding modes, binding affinities and "hot spots" for protein-ligand complexes using a knowledge-based scoring function.
Persp. Drug Design Discov. 2000, 20, 115-144. [PDF]
 
5. Klebe, G., Grädler, U., Grüneberg, S., Krämer, O., Gohlke, H.
Understanding receptor-ligand interactions as a prerequisite for virtual screening.
In Virtual Screening for Bioactive Molecules (Böhm, H. J., Schneider, S., Ed.), S. 207-227, Wiley-VCH, Weinheim, 2000.
 
4. Gohlke, H., Hendlich, M., Klebe, G.
Knowledge-based scoring function to predict protein-ligand interactions.
J. Mol. Biol. 2000, 295, 337-356. [PDF]
 

1999


3. Klebe, G., Böhm, M., Dullweber, F., Grädler, U., Gohlke, H., Hendlich, M.
Structural and energetic aspects of protein-ligand binding in drug design.
In Molecular Modelling and Prediction of Bioactivity (Gundertofte, K., Jorgensen, F., Ed.), S. 103-110, KLUWER Academic / Plenum Publ., New York, 1999.
 
2. Gohlke, H., Immel, S., Lichtenthaler, F.W.
Conformations and lipophilicity profiles of some cyclic ß-(1->3)- and ß-(1->6)-linked oligogalactofuranosides.
Carbohydr. Res. 1999, 321, 96-104. [PDF]
 
1. Gohlke, H., Immel, S., Lichtenthaler, F.W., Schmitt, G.E.
ß-(1->3)- and ß-(1->6)-linked cyclogalactofuranosides: conformations and molecular shapes.
In Proceedings of the 9th International Symposium on Cyclodextrins (J.J. Torres-Labandeira, J. L. Vila Jato, Ed.), S. 63-68, Kluwer Acad. Publ., Dordrecht, 1998