Publications

Peer-Reviewed Journals

Two-Step Covalent Docking with Attracting Cavities M. Goullieux, V. Zoete, U. F. Röhrig, J. Chem. Inf. Model. (2023), doi: 10.1021/acs.jcim.3c01055 (OPEN ACCESS)
SwissParam 2023: A Modern Web-Based Tool for Efficient Small-Molecule Parametrization M. Bugnon, M. Goullieux, U. F. Röhrig, M. Perez, A. Daina, O. Michielin, V. Zoete, J. Chem. Inf. Model. 63, 6469-6475 (2023), doi: 10.1021/acs.jcim.3c01053
Attracting Cavities 2.0: Improving the flexibility and Robustness for Small-Molecule Docking U. F. Röhrig, M. Goullieux, M. Bugnon, V. Zoete, J. Chem. Inf. Model. 63, 3925-3940 (2023), doi: 10.1021/acs.jcim.3c00054
Structure-based optimization of type III indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors U.F. Röhrig, S.R. Majjigapu, P. Vogel, A. Reynaud, F. Pojer, N. Dilek, P. Reichenbach, K. Ascenção, M. Irving, G. Coukos, O. Michielin, V. Zoete, J. Enz. Inh. Med. Chem. 37, 1773-1811 (2022), doi: 10.1080/14756366.2022.2089665 (OPEN ACCESS)
Structure and Plasticity of Indoleamine 2,3-Dioxygenase 1 (IDO1) U.F. Röhrig, O. Michielin, V. Zoete, J. Med. Chem. 64, 17690–17705 (2021), doi: 10.1021/acs.jmedchem.1c01665 (OPEN ACCESS)
Azole-Based Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors U.F. Röhrig, S.R. Majjigapu, A. Reynaud, F. Pojer, N. Dilek, P. Reichenbach, K. Ascencao, M. Irving, G. Coukos, P. Vogel, O. Michielin, V. Zoete, J. Med. Chem. 64, 2205-2227 (2021), doi: 10.1021/acs.jmedchem.0c01968 (OPEN ACCESS)
Inhibition Mechanisms of Indoleamine 2,3-Dioxygenase 1 (IDO1) U.F. Röhrig, A. Reynaud, S.R. Majjigapu, P. Vogel, F. Pojer, V. Zoete, J. Med. Chem. 62, 8784–8795 (2019), doi: 10.1021/acs.jmedchem.9b00942
Tryptophan metabolism as a common therapeutic target in cancer, neurodegeneration and beyond M. Platten, E. A. A. Nollen, U. F. Röhrig, F. Fallarino, C. Opitz, Nat. Rev. Drug Discov. 18, 379–401 (2019), doi: 10.1038/s41573-019-0016-5
The conserved threonine-rich region of the HCF-1PRO repeat activates promiscuous OGT:UDP-GlcNAc glycosylation and proteolysis activities V. Kapuria, U. F. Röhrig, P. Waridel, F. Lammers, V.S. Borodkin, D.M.F. van Aalten, V. Zoete, W. Herr, J. Biol. Chem. 293, 17754-17768 (2018), doi: 10.1074/jbc.RA118.004185 (OPEN ACCESS)
The Binding Mode of N-Hydroxyamidines to Indoleamine 2,3-Dioxygenase 1 (IDO1) U. F. Röhrig, V. Zoete, O. Michielin, Biochemistry 56, 4323–4325 (2017), doi: 10.1021/acs.biochem.7b00586
On-The-Fly QM/MM Docking with Attracting Cavities P. Chaskar, V. Zoete, U. F. Röhrig, J. Chem. Inf. Model. 57, 73-84 (2017) doi: 10.1021/acs.jcim.6b00406
1,2,3-Triazoles as Inhibitors of Indoleamine 2,3-Dioxygenase 2 (IDO2) U. F. Röhrig, S. R. Majjigapu, D. Caldelari, N. Dilek, P. Reichenbach, K. Ascencao, M. Irving, G. Coukos, P. Vogel, V. Zoete, O. Michielin, Bioorg. Med. Chem. Lett. 26, 4330-4333 (2016), doi: 10.1016/j.bmcl.2016.07.031
Proteolysis of HCF-1 by Ser/Thr glycosylation-incompetent O-GlcNAc transferase:UDP-GlcNAc complexes V. Kapuria, U. F. Röhrig, T. Bhuiyan, V.S. Borodkin, D.M.F. van Aalten, V. Zoete, W. Herr, Genes. Dev. 30, 960-972 (2016), doi: 10.1101/gad.275925.115 (OPEN ACCESS)
Attracting Cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape V. Zoete, T. Schuepbach, C. Bovigny, P. Chaskar, A. Daina, U. F. Röhrig, O. Michielin, J. Comput. Chem. 37, 437-447 (2016), doi: 10.1002/jcc.24249 (OPEN ACCESS)
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases SIB Swiss Institute of Bioinformatics Members, Nucleic Acids Res. 44, D27-D37 (2016), doi: 10.1093/nar/gkv1310 (OPEN ACCESS)
Single amino acid charge switch defines clinically distinct proline-serine-threonine phosphatase-interacting protein 1 (PSTPIP1)-associated inflammatory diseases D. Holzinger, S.K. Fassl, W. de Jager, P. Lohse, U.F. Röhrig, M. Gattorno, A. Omenetti, S. Chiesa, F. Schena, J. Austermann, T. Vogl, D.B. Kuhns, S.M. Holland, C. Rodríguez-Gallego, R. López-Almaraz, J.I. Arostegui, E. Colino, R. Roldan, S. Fessatou, B. Isidor, S. Poignant, K. Ito, H.-J. Epple, J.A. Bernstein, M. Jeng, J. Frankovich, G. Lionetti, J.A. Church, P.Y. Ong, M. LaPlant, M. Abinun, R. Skinner, V. Bigley, U.J. Sachs, C. Hinze, E. Hoppenreijs, J. Ehrchen, D. Foell, J.J. Chae, A. Ombrello, I. Aksentijevich, C. Sunderkoetter, J. Roth, J. Allergy Clin. Immunol. 136, 1337–1345 (2015), doi: 10.1016/j.jaci.2015.04.016
Challenges in the Discovery of Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors U. F. Röhrig, S. R. Majjigapu, P. Vogel, V. Zoete, O. Michielin, J. Med. Chem. 58, 9421–9437 (2015), doi: 10.1021/acs.jmedchem.5b00326 (OPEN ACCESS)
Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function P. Chaskar, V. Zoete, U. F. Röhrig, J. Chem. Inf. Model. 54, 3137-3152 (2014), doi: 10.1021/ci5004152
Detailed Analysis and Follow-Up Studies of a High-Throughput Screening for Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors U.F. Röhrig, Somi Reddy Majjigapu, Marc Chambon, Sylvian Bron, Luc Pilotte, Didier Colau, Benoit J. Van den Eynde, Gerardo Turcatti, Pierre Vogel, Vincent Zoete, Olivier Michielin, Eur. J. Med. Chem. 84, 284-301 (2014), doi: 10.1016/j.ejmech.2014.06.078
Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle P. Campomanes , M. Neri , B.A.C. Horta , U.F. Röhrig , S. Vanni , I. Tavernelli , U. Rothlisberger, J. Am. Chem. Soc. 136, 3842–3851 (2014), doi: 10.1021/ja411303v
Rational Design of 4-Aryl-1,2,3-Triazoles for Indoleamine 2,3-Dioxygenase 1 Inhibition U. F. Röhrig, S. Reddy Majjigapu, A. Grosdidier, S. Bron, V. Stroobant, L. Pilotte, D. Colau, P. Vogel, B. J. Van den Eynde, V. Zoete, O. Michielin, J. Med. Chem. 55, 5270–5290 (2012), doi:10.1021/jm300260v
Molecular Mechanism of a Green-Shifted, pH-Dependent Red Fluorescent Protein mKate Variant Q. Wang, L. J. Byrnes, B. Shui, U. F. Röhrig, A. Sing, D. M. Chudakov, S. Lukyanov, W. R. Zipfel, M. I. Kotlikoff, H, Sondermann, PLoS ONE 6, e23513 (2011), doi: 10.1371/journal.pone.0023513
Structure-function analyses point to a polynucleotide-accommodating groove essential for APOBEC3A restriction activities Y. Bulliard, I. Narvaiza, A. Bertero, S. Peddi, U. F. Röhrig, M. Ortiz, V. Zoete, N. Castro-Diaz, P. Turelli, A. Telenti, O. Michielin, M. D. Weitzman, D. Trono, J. Virol. 85, 1765 (2011), doi:10.1128/JVI.01651-10
Frequent MAGE mutations in human melanoma O. L. Caballero, Q. Zhao, D. Rimoldi, B. J. Stevenson, S. Svobodová, S. Devalle, U. F. Röhrig, A. Pagotto, O. Michielin, D. Speiser, J. D. Wolchok, Ca. Liu, T. Pejovic, K. O. Odunsi, F. Brasseur, B. J. Van den Eynde, L. J. Old, X. Lu, J. Cebon, R. L. Strausberg, A. J. Simpson, PloS ONE 5, e12773 (2010), doi:10.1371/journal.pone.0012773
Rational Design of Indoleamine 2,3-Dioxygenase Inhibitors U. F. Röhrig, A. Loay, A. Grosdidier, P. Larrieu, V. Stroobant, D. Colau, V. Cerundolo, A. J. Simpson, P. Vogel, B. Van den Eynde, V. Zoete, O. Michielin, J. Med. Chem. 53, 1172–1189 (2010), doi:10.1021/jm9014718
Functional Analysis and Structural Modeling of Human APOBEC3G Reveals the Role of Evolutionarily Conserved Elements in HIV-1 and Alu Inhibition Y. Bulliard, P. Turelli, U. F. Röhrig, V. Zoete, B. Mangeat, O. Michielin, D. Trono, J. Virol. 83, 12611-12621 (2009), doi:10.1128/JVI.01491-09
Docking to Heme Proteins U. F. Röhrig, A. Grosdidier, V. Zoete, O. Michielin, J. Comput. Chem. 30, 2305-2315 (2009), doi:10.1002/jcc.21244

NMR Chemical Shifts of the Rhodopsin Chromophore in the Dark State and in Bathorhodopsin: A Hybrid QM/MM Molecular Dynamics Study U. F. Röhrig and D. Sebastiani, J. Phys. Chem. B 112, 1267-1274 (2008), doi:10.1021/jp075662q
CNDOL: A fast and reliable method for the calculation of electronic properties of very large systems. Applications to retinal binding pocket in rhodopsin and gas phase porphine L.A. Montero-Cabrera, U. Röhrig, J.A. Padrón-Garcia, R. Crespo-Otero, A.L. Montero-Alejo, J.M. Garcia de la Vega, M. Chergui, U. Rothlisberger, J. Chem. Phys. 127, 145102 (2007), doi:10.1063/1.2761869
Stability and Structure of Oligomers of the Alzheimer Peptide Ab16-22: From the Dimer to the 32-mer U. F. Röhrig, A. Laio, N. Tantalo, M. Parrinello, R. Petronzio, Biophys. J. 91, 3217-3229 (2006), doi:10.1529/biophysj.106.088542
Solvent and Protein Effects on the Structure and Dynamics of the Rhodopsin Chromophore U. F. Röhrig, L. Guidoni, U. Röthlisberger, ChemPhysChem 6, 1836-1847 (2005), doi:10.1002/cphc.200500066
Molecular Dynamics in Electronically Excited States using Time-Dependent Density Functional Theory I. Tavernelli, U. F. Röhrig, U. Röthlisberger, Mol. Phys. 103, 963-981 (2005), doi:10.1080/00268970512331339378
Optical Properties of Molecules in Solution via Hybrid TDDFT/MM Simulations M. Sulpizi, U. F. Röhrig, J. Hutter, U. Röthlisberger, Int. J. Quant. Chem. 101, 671-682 (2005), doi:10.1002/qua.20325
A Molecular Spring for Vision U. F. Röhrig, L. Guidoni, A. Laio, I. Frank, U. Röthlisberger, J. Am. Chem. Soc. 126, 15328-15329 (2004), doi:10.1021/ja048265r
QM/MM Car-Parrinello Molecular Dynamics Study of the Solvent Effects on the Ground State and on the First Excited Singlet State of Acetone in Water U. F. Röhrig, I. Frank, J. Hutter, A. Laio, J. VandeVondele, U. Röthlisberger, ChemPhysChem 4, 1177-1182 (2003), doi:10.1002/cphc.200300650

Organic Chromophores under Tensile Stress U. F. Röhrig, U. Troppmann, I. Frank, Chem. Phys. 289, 381-388 (2003), doi:10.1016/S0301-0104(03)00085-5
Early Steps of the Intramolecular Signal Transduction in Rhodopsin Explored by Molecular Dynamics Simulations U. F. Röhrig, L. Guidoni, U. Röthlisberger, Biochemistry 41, 10799-10809 (2002), doi:10.1021/bi026011h
First-Principles Molecular Dynamics Study of a Polymer under Tensile Stress U. F. Röhrig, I. Frank, J. Chem. Phys. 115, 8670-8674 (2001), doi:10.1063/1.1411995
Syntheses of Phosphinine-Based Tripodal Ligands U. F. Röhrig, N. Mezailles, N. Maigrot, L. Ricard, F. Mathey, P. Le Floch, Eur. J. Inorg. Chem. 12, 2565-2571 (2000), doi:10.1002/1099-0682(200012)2000:12<2565::AID-EJIC2565>3.0.CO;2-X

Reviews

Quantum Mechanical/Molecular Mechanical (QM/MM) Car-Parrinello Simulations in Excited States M.-E. Moret, E. Tapavicza, L. Guidoni, U. F. Röhrig, M. Sulpizi, I. Tavernelli, U. Röthlisberger, CHIMIA 59, 493-498 (2005), doi:10.2533/000942905777676128
Hybrid QM/MM Car-Parrinello simulations of catalytic and enzymatic reactions M. C. Colombo, L. Guidoni, A. Laio, A. Magistrato, P. Maurer, S. Piana, U. F. Röhrig, K. Spiegel, M. Sulpizi, J. VandeVondele, M. Zumstein and U. Röthlisberger, CHIMIA 56, 13-19 (2002).

Book Chapters

Structural Prediction of Peptide-MHC Binding Modes M.A.S Perez, M.A. Cuendet, U.F. Röhrig, O. Michielin, V. Zoete, In: T. Simonson (ed) Computational Peptide Science: Methods and Protocols. Methods in Molecular Biology 2405, 245-282, Humana, New York (2022), doi: 10.1007/978-1-0716-1855-4_13
Computer-Aided Drug Design for Cancer Therapy A. Daina, U.F. Röhrig, V. Zoete, In: O. Wolkenhauer (ed) Systems Medicine 2, 386-401, Ed.: O. Wolkenhauer, Academic Press (2021), doi :10.1016/B978-0-12-801238-3.11670-8
Inhibitors of the Kynurenine Pathway U. F. Röhrig, V. Zoete, O. Michielin, In: Waring M.J. (eds) Cancer II. Topics in Medicinal Chemistry, 28. Springer, Cham (2017), doi:10.1007/7355_2017_22
Molecular Modeling of Proteins: From Simulations to Drug Design Applications V. Zoete, M. Cuendet, U. F. Röhrig, A. Grosdidier, O. Michielin, Bioinformatics A Swiss Perspective, R. D. Appel & E. Feytmans (Eds.), World Scientific (2009).
In Silico Dynamic Studies of Cis-Trans Isomerization in Organic and Biological Systems U. F. Röhrig, I. Tavernelli, U. Röthlisberger, Cis-Trans Isomerization in Biochemistry, C. Dugave (Ed.), Wiley-VCH, Weinheim, Germany (2006), doi:10.1002/9783527609338.ch7
QM/MM Simulation of the First Step of Vision U. F. Röhrig, S. Grimm, I. Frank, L. Guidoni, A. Laio, U. Röthlisberger, High Performance Computing in Science and Engineering, Munich 2004, S. Wagner, W. Hanke, A. Bode, F. Durst (Eds.), Springer, Heidelberg (2005), doi:10.1007/3-540-26657-7_21
QM/MM Study of Rhodopsin U. F. Röhrig, C. Nonnenberg, I. Frank, L. Guidoni, U. Röthlisberger, High Performance Computing in Science and Engineering, Munich 2002, S. Wagner, W. Hanke, A. Bode, F. Durst (Eds.), Springer, Heidelberg (2003).