50. Bringing Molecular Dynamics Simulations into View.

Hildebrand PW, Rose AS, Tiemann JKS.

Trends Biochem Sci. 2019 Jul 10. pii: S0968-0004(19)30137-9. doi: 10.1016/j.tibs.2019.06.004. PMID: 31301982

49. Structural Insights into the Process of GPCR-G Protein Complex Formation.

Liu X, Xu X, Hilger D, Aschauer P, Tiemann JKS, Du Y, Liu H, Hirata K, Sun X, Guixà-González R, Mathiesen JM, Hildebrand PW, Kobilka BK.

Cell. 2019 May 16;177(5):1243-1251.e12. doi: 10.1016/j.cell.2019.04.021 Epub 2019 May 9. PMID: 31080070

48. FragFit: a Web-Application for Interactive Modeling of Protein Segments into Cryo-EM Density Maps.

Tiemann JK, Rose AS, Ismer J, Darvish MD, Hilal T, Spahn CM, Hildebrand PW.

Nucleic Acids Res. 2018 Jul 2;46(W1):W310-W314. doi: 10.1093/nar/gky424. PMID: 29788317

47. Binding, Thermodynamics, and Selectivity of a Non-peptide Antagonist to the Melanocortin-4 Receptor.

Saleh N, Kleinau G, Heyder N, Clark T, Hildebrand PW, Scheerer P.

Front Pharmacol. 2018 Jun 1;9:560. doi: 10.3389/fphar.2018.00560 . eCollection 2018. PMID: 29910730

46. Structural Basis for the Interaction of the Beta-Secretase with Copper.

Bittner HJ, Guixà-González R, Hildebrand PW.

Biochim Biophys Acta Biomembr. 2018 May;1860(5):1105-1113. doi: 10.1016/j.bbamem.2018.01.019 . Epub 2018 Jan 31. PMID: 29391167

45. The Arrestin-1 Finger Loop Interacts with two Distinct Conformations of Active Rhodopsin.

Elgeti M, Kazmin R, Rose AS, Szczepek M, Hildebrand PW, Bartl FJ, Scheerer P, Hofmann KP.

J Biol Chem. 2018 Mar 23;293(12):4403-4410. doi: 10.1074/jbc.M117.817890 . Epub 2018 Jan 23. PMID: 29363577

44. Multiple Binding Sites Contribute to the Mechanism of Mixed Agonistic and Positive Allosteric Modulators of the Cannabinoid CB1 Receptor.

Saleh N, Hucke O, Kramer G, Schmidt E, Montel F, Lipinski R, Ferger B, Clark T, Hildebrand PW, Tautermann CS.

Angew Chem Int Ed Engl. 2018 Mar 1;57(10):2580-2585. doi: 10.1002/anie.201708764 . Epub 2018 Feb 2. PMID: 29314474

43. MDsrv: Viewing and Sharing Molecular Dynamics Simulations on the Web.

Tiemann JKS, Guixà-González R, Hildebrand PW, Rose AS.

Nat Methods. 2017 Nov 30;14(12):1123-1124. doi: 10.1038/nmeth.4497 . No abstract available. PMID: 29190271

42. A Fragment Based Method for Modeling of Protein Segments into Cryo-EM Density Maps.

Ismer J, Rose AS, Tiemann JKS, Hildebrand PW.

BMC Bioinformatics. 2017 Nov 13;18(1):475. doi: 10.1186/s12859-017-1904-5. PMID: 29132296

41. GPCR-SSFE 2.0-a Fragment-Based Molecular Modeling Web Tool for Class A G-Protein Coupled Receptors.

Worth CL, Kreuchwig F, Tiemann JKS, Kreuchwig A, Ritschel M, Kleinau G, Hildebrand PW, Krause G.

Nucleic Acids Res. 2017 Jul 3;45(W1):W408-W415. doi: 10.1093/nar/gkx399. PMID: 28582569

40. Membrane Cholesterol Access into a G-protein-Coupled Receptor.

Guixà-González R, Albasanz JL, Rodriguez-Espigares I, Pastor M, Sanz F, Martí-Solano M, Manna M, Martinez-Seara H, Hildebrand PW, Martín M, Selent J.

Nat Commun. 2017 Feb 21;8:14505. doi: 10.1038/ncomms14505. PMID: 28220900

39. SL2: an Interactive Webtool for Modeling of Missing Segments in Proteins.

Ismer J, Rose AS, Tiemann JK, Goede A, Preissner R, Hildebrand PW.

Nucleic Acids Res. 2016 Jul 8;44(W1):W390-4. doi: 10.1093/nar/gkw297 . Epub 2016 Apr 21. PMID: 27105847

38. Structures of Ribosome-Bound Initiation Factor 2 Reveal the Mechanism of Subunit Association.

Sprink T, Ramrath DJ, Yamamoto H, Yamamoto K, Loerke J, Ismer J, Hildebrand PW, Scheerer P, Bürger J, Mielke T, Spahn CM.

Sci Adv. 2016 Mar 4;2(3):e1501502. doi: 10.1126/sciadv.1501502 . eCollection 2016 Mar. PMID: 26973877

37. Additive Loss-of-Function Proteasome Subunit Mutations in CANDLE/PRAAS Patients Promote Type I IFN Production.

Brehm A, Liu Y, Sheikh A, Marrero B, Omoyinmi E, Zhou Q, Montealegre G, Biancotto A, Reinhardt A, de Jesus AA, Pelletier M, Tsai WL, Remmers EF, Kardava L, Hill S, Kim H, Lachmann HJ, Megarbane A, Chae JJ, Brady J, Castillo RD, Brown D, Casano AV, Gao L, Chapelle D, Huang Y, Stone D, Chen Y, Sotzny F, Lee CC, Kastner DL, Torrelo A, Zlotogorski A, Moir S, Gadina M, McCoy P, Wesley R, Rother KI, Hildebrand PW, Brogan P, Krüger E, Aksentijevich I, Goldbach-Mansky R.

J Clin Invest. 2016 Feb;126(2):795. doi: 10.1172/JCI86020 . Epub 2016 Feb 1. No abstract available. PMID: 26829627

36. Molecular Architecture of the Ribosome-Bound Hepatitis C Virus Internal Ribosomal Entry Site RNA.

Yamamoto H, Collier M, Loerke J, Ismer J, Schmidt A, Hilal T, Sprink T, Yamamoto K, Mielke T, Bürger J, Shaikh TR, Dabrowski M, Hildebrand PW, Scheerer P, Spahn CM.

EMBO J. 2015 Dec 14;34(24):3042-58. doi: 10.15252/embj.201592469 . Epub 2015 Nov 24. PMID: 26604301

35. Structural Mechanism of the Interaction of Alzheimer Disease Aβ Fibrils with the Non-Steroidal Anti-Inflammatory Drug (NSAID) Sulindac Sulfide.

Prade E, Bittner HJ, Sarkar R, Lopez Del Amo JM, Althoff-Ospelt G, Multhaup G, Hildebrand PW, Reif B.

J Biol Chem. 2015 Nov 27;290(48):28737-45. doi: 10.1074/jbc.M115.675215 . Epub 2015 Sep 28. PMID: 26416887

34. Role of Structural Dynamics at the Receptor G Protein Interface for Signal Transduction.

Rose AS, Zachariae U, Grubmüller H, Hofmann KP, Scheerer P, Hildebrand PW.

PLoS One. 2015 Nov 25;10(11):e0143399. doi: 10.1371/journal.pone.0143399 . eCollection 2015. PMID: 26606751

33. Additive Loss-of-Function Proteasome Subunit Mutations in CANDLE/PRAAS Patients Promote Type I IFN Production.

Brehm A, Liu Y, Sheikh A, Marrero B, Omoyinmi E, Zhou Q, Montealegre G, Biancotto A, Reinhardt A, Almeida de Jesus A, Pelletier M, Tsai WL, Remmers EF, Kardava L, Hill S, Kim H, Lachmann HJ, Megarbane A, Chae JJ, Brady J, Castillo RD, Brown D, Casano AV, Gao L, Chapelle D, Huang Y, Stone D, Chen Y, Sotzny F, Lee CC, Kastner DL, Torrelo A, Zlotogorski A, Moir S, Gadina M, McCoy P, Wesley R, Rother KI, Hildebrand PW, Brogan P, Krüger E, Aksentijevich I, Goldbach-Mansky R.

J Clin Invest. 2015 Nov 2;125(11):4196-211. doi: 10.1172/JCI81260 . Epub 2015 Oct 20. Erratum in: J Clin Invest. 2016 Feb;126(2):795. Rother, Kristina [corrected to Rother, Kristina I]. PMID: 26524591

32. Aβ42-Oligomer Interacting Peptide (AIP) Neutralizes Toxic Amyloid-β42 Species and Protects Synaptic Structure and Function.

Barucker C, Bittner HJ, Chang PK, Cameron S, Hancock MA, Liebsch F, Hossain S, Harmeier A, Shaw H, Charron FM, Gensler M, Dembny P, Zhuang W, Schmitz D, Rabe JP, Rao Y, Lurz R, Hildebrand PW, McKinney RA, Multhaup G.

Sci Rep. 2015 Oct 29;5:15410. doi: 10.1038/srep15410. PMID: 26510576

31. The Activation Pathway of Human Rhodopsin in Comparison to Bovine Rhodopsin.

Kazmin R, Rose A, Szczepek M, Elgeti M, Ritter E, Piechnick R, Hofmann KP, Scheerer P, Hildebrand PW, Bartl FJ.

J Biol Chem. 2015 Aug 14;290(33):20117-27. doi: 10.1074/jbc.M115.652172 . Epub 2015 Jun 23. PMID: 26105054

30. NGL Viewer: a Web Application for Molecular Visualization.

Rose AS, Hildebrand PW.

Nucleic Acids Res. 2015 Jul 1;43(W1):W576-9. doi: 10.1093/nar/gkv402 . Epub 2015 Apr 29. PMID: 25925569

29. Impact of Amyloid Precursor Protein Hydrophilic Transmembrane Residues on Amyloid-Beta Generation.

Oestereich F, Bittner HJ, Weise C, Grohmann L, Janke LK, Hildebrand PW, Multhaup G, Munter LM.

Biochemistry. 2015 May 5;54(17):2777-84. doi: 10.1021/acs.biochem.5b00217 . Epub 2015 Apr 23. PMID: 25875527

28. Structure-Based Biophysical Analysis of the Interaction of Rhodopsin with G Protein and Arrestin.

Sommer ME, Elgeti M, Hildebrand PW, Szczepek M, Hofmann KP, Scheerer P.

Methods Enzymol. 2015;556:563-608. doi: 10.1016/bs.mie.2014.12.014 . Epub 2015 Mar 6. PMID: 25857800

27. Crystal Structure of a Common GPCR-Binding Interface for G Protein and Arrestin.

Szczepek M, Beyrière F, Hofmann KP, Elgeti M, Kazmin R, Rose A, Bartl FJ, von Stetten D, Heck M, Sommer ME, Hildebrand PW, Scheerer P.

Nat Commun. 2014 Sep 10;5:4801. doi: 10.1038/ncomms5801. PMID: 25205354

26. Position of Transmembrane Helix 6 Determines Receptor G Protein Coupling Specificity.

Rose AS, Elgeti M, Zachariae U, Grubmüller H, Hofmann KP, Scheerer P, Hildebrand PW.

J Am Chem Soc. 2014 Aug 13;136(32):11244-7. doi: 10.1021/ja5055109 . Epub 2014 Jul 31. PMID: 25046433

25. Regulation of the Mammalian Elongation Cycle by Subunit Rolling: a Eukaryotic-Specific Ribosome Rearrangement.

Budkevich TV, Giesebrecht J, Behrmann E, Loerke J, Ramrath DJ, Mielke T, Ismer J, Hildebrand PW, Tung CS, Nierhaus KH, Sanbonmatsu KY, Spahn CM.

Cell. 2014 Jul 3;158(1):121-31. doi: 10.1016/j.cell.2014.04.044. PMID: 24995983

24. MP:PD--a Data Base of Internal Packing Densities, Internal Packing Defects and Internal Waters of Helical Membrane Proteins.

Rose A, Theune D, Goede A, Hildebrand PW.

Nucleic Acids Res. 2014 Jan;42(Database issue):D347-51. doi: 10.1093/nar/gkt1062 . Epub 2013 Nov 4. PMID: 24194596

23. Model Peptides Uncover the Role of the β-Secretase Transmembrane Sequence in Metal Iion Mediated Oligomerization.

Munter LM, Sieg H, Bethge T, Liebsch F, Bierkandt FS, Schleeger M, Bittner HJ, Heberle J, Jakubowski N, Hildebrand PW, Multhaup G.

J Am Chem Soc. 2013 Dec 26;135(51):19354-61. doi: 10.1021/ja410812r . Epub 2013 Dec 13. PMID: 24304299

22. Precision vs Flexibility in GPCR Signaling.

Elgeti M, Rose AS, Bartl FJ, Hildebrand PW, Hofmann KP, Heck M.

J Am Chem Soc. 2013 Aug 21;135(33):12305-12. doi: 10.1021/ja405133k . Epub 2013 Aug 9. PMID: 23883288

21. Voronoia4RNA--a Database of Atomic Packing Densities of RNA Structures and their Complexes.

Ismer J, Rose AS, Tiemann JK, Goede A, Rother K, Hildebrand PW.

Nucleic Acids Res. 2013 Jan;41(Database issue):D280-4. doi: 10.1093/nar/gks1061 . Epub 2012 Nov 17. PMID: 23161674

20. Novel APP/Aβ Mutation K16N Produces Highly Toxic Heteromeric Aβ Oligomers.

Kaden D, Harmeier A, Weise C, Munter LM, Althoff V, Rost BR, Hildebrand PW, Schmitz D, Schaefer M, Lurz R, Skodda S, Yamamoto R, Arlt S, Finckh U, Multhaup G.

EMBO Mol Med. 2012 Jul;4(7):647-59. doi: 10.1002/emmm.201200239 . Epub 2012 Apr 19. PMID: 22514144

19. Effect of Channel Mutations on the Uptake and Release of the Retinal Ligand in Opsin.

Piechnick R, Ritter E, Hildebrand PW, Ernst OP, Scheerer P, Hofmann KP, Heck M.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5247-52. doi: 10.1073/pnas.1117268109 . Epub 2012 Mar 19. PMID: 22431612

18. Structural Basis for the Binding of IRES RNAs to the Head of the Ribosomal 40S Subunit.

Muhs M, Yamamoto H, Ismer J, Takaku H, Nashimoto M, Uchiumi T, Nakashima N, Mielke T, Hildebrand PW, Nierhaus KH, Spahn CM.

Nucleic Acids Res. 2011 Jul;39(12):5264-75. doi: 10.1093/nar/gkr114 . Epub 2011 Mar 4. PMID: 21378123

17. The Amyloid Precursor Protein C-Terminal Fragment C100 Occurs in Monomeric and Dimeric Stable Conformations and Binds y-Secretase Modulators.

Botev A, Munter LM, Wenzel R, Richter L, Althoff V, Ismer J, Gerling U, Weise C, Koksch B, Hildebrand PW, Bittl R, Multhaup G.

Biochemistry. 2011 Feb 8;50(5):828-35. doi: 10.1021/bi1014002 . Epub 2011 Jan 11. PMID: 21186781

16. Head Swivel on the Ribosome Facilitates Translocation by Means of Intra-Subunit tRNA Hybrid Sites.

Ratje AH, Loerke J, Mikolajka A, Brünner M, Hildebrand PW, Starosta AL, Dönhöfer A, Connell SR, Fucini P, Mielke T, Whitford PC, Onuchic JN, Yu Y, Sanbonmatsu KY, Hartmann RK, Penczek PA, Wilson DN, Spahn CM.

Nature. 2010 Dec 2;468(7324):713-6. doi: 10.1038/nature09547. PMID: 21124459

15. Amyloid Beta 42 Peptide (Abeta42)-Lowering Compounds Directly Bind to Abeta and Interfere with Amyloid Precursor Protein (APP) Transmembrane Dimerization.

Richter L, Munter LM, Ness J, Hildebrand PW, Dasari M, Unterreitmeier S, Bulic B, Beyermann M, Gust R, Reif B, Weggen S, Langosch D, Multhaup G.

Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14597-602. doi: 10.1073/pnas.1003026107 . Epub 2010 Aug 2. PMID: 20679249

14. Aberrant Amyloid Precursor Protein (APP) Processing in Hereditary Forms of Alzheimer Disease Caused by APP Familial Alzheimer Disease Mutations Can be Rescued by Mutations in the APP GxxxG Motif.

Munter LM, Botev A, Richter L, Hildebrand PW, Althoff V, Weise C, Kaden D, Multhaup G.

J Biol Chem. 2010 Jul 9;285(28):21636-43. doi: 10.1074/jbc.M109.088005 . Epub 2010 May 7. PMID: 20452985

13. MPlot--a Server to Analyze and Visualize Tertiary Structure Contacts and Geometrical Features of Helical Membrane Proteins.

Rose A, Goede A, Hildebrand PW.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W602-8. doi: 10.1093/nar/gkq401 . Epub 2010 May 19. PMID: 20484376

12. A G Protein-Coupled Receptor at Work: the Rhodopsin Model.

Hofmann KP, Scheerer P, Hildebrand PW, Choe HW, Park JH, Heck M, Ernst OP.

Trends Biochem Sci. 2009 Nov;34(11):540-52. doi: 10.1016/j.tibs.2009.07.005 . Epub 2009 Oct 21. Review. PMID: 19836958

11. RHYTHM--a Server to Predict the Orientation of Transmembrane Helices in Channels and Membrane-Coils.

Rose A, Lorenzen S, Goede A, Gruening B, Hildebrand PW.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W575-80. doi: 10.1093/nar/gkp418 . Epub 2009 May 22. PMID: 19465378

10. SuperLooper--a Prediction Server for the Modeling of Loops in Globular and Membrane Proteins.

Hildebrand PW, Goede A, Bauer RA, Gruening B, Ismer J, Michalsky E, Preissner R.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W571-4. doi: 10.1093/nar/gkp338 . Epub 2009 May 8. PMID: 19429894

9. Structural and Kinetic Modeling of an Activating Helix Switch in the Rhodopsin-Transducin Interface.

Scheerer P, Heck M, Goede A, Park JH, Choe HW, Ernst OP, Hofmann KP, Hildebrand PW.

Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10660-5. doi: 10.1073/pnas.0900072106 . Epub 2009 Jun 17. PMID: 19541654

8. Role of Amyloid-Beta Glycine 33 in Oligomerization, Toxicity, and Neuronal Plasticity.

Harmeier A, Wozny C, Rost BR, Munter LM, Hua H, Georgiev O, Beyermann M, Hildebrand PW, Weise C, Schaffner W, Schmitz D, Multhaup G.

J Neurosci. 2009 Jun 10;29(23):7582-90. doi: 10.1523/JNEUROSCI.1336-09.2009. PMID: 19515926

7. Voronoia: Analyzing Packing in Protein Structures.

Rother K, Hildebrand PW, Goede A, Gruening B, Preissner R.

Nucleic Acids Res. 2009 Jan;37(Database issue):D393-5. doi: 10.1093/nar/gkn769 . Epub 2008 Oct 23. PMID: 18948293

6. A Ligand Channel through the G Protein Coupled Receptor Opsin.

Hildebrand PW, Scheerer P, Park JH, Choe HW, Piechnick R, Ernst OP, Hofmann KP, Heck M.

PLoS One. 2009;4(2):e4382. doi: 10.1371/journal.pone.0004382 . Epub 2009 Feb 5. PMID: 19194506

5. Crystal Structure of Opsin in its G-Protein-Interacting Conformation.

Scheerer P, Park JH, Hildebrand PW, Kim YJ, Krauss N, Choe HW, Hofmann KP, Ernst OP.

Nature. 2008 Sep 25;455(7212):497-502. doi: 10.1038/nature07330. PMID: 18818650

4. Hydrogen-Bonding and Packing Features of Membrane Proteins: Functional Implications.

Hildebrand PW, Günther S, Goede A, Forrest L, Frömmel C, Preissner R.

Biophys J. 2008 Mar 15;94(6):1945-53. doi: 10.1529/biophysj.107.110395. Epub 2007 Oct 5. PMID: 17921213

3. Analysis and Prediction of Helix-Helix Interactions in Membrane Channels and Transporters.

Hildebrand PW, Lorenzen S, Goede A, Preissner R.

Proteins. 2006 Jul 1;64(1):253-62. DOI: 10.1002/prot.20959 PMID: 16555307

2. Molecular Packing and Packing Defects in Helical Membrane Proteins.

Hildebrand PW, Rother K, Goede A, Preissner R, Frömmel C.

Biophys J. 2005 Mar;88(3):1970-7. DOI: 10.1529/biophysj.104.049585 Epub 2004 Nov 19. PMID: 15556989

1. Structural Features of Transmembrane Helices.

Hildebrand PW, Preissner R, Frömmel C.

FEBS Lett. 2004 Feb 13;559(1-3):145-51. DOI: 10.1016/S0014-5793(04)00061-4 PMID: 14960323