Ute Friederike Röhrig

Publications | Mémoires et thèses

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36 publications

2018 | 2017 | 2016 | 2015 | 2014 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 |
The conserved threonine-rich region of the HCF-1<sub>PRO</sub> repeat activates promiscuous OGT:UDP-GlcNAc glycosylation and proteolysis activities.
Kapuria V., Röhrig U.F., Waridel P., Lammers F., Borodkin V.S., van Aalten DMF, Zoete V., Herr W., 2018/11/16. The Journal of biological chemistry, 293 (46) pp. 17754-17768. Peer-reviewed.
 
On-the-Fly QM/MM Docking with Attracting Cavities.
Chaskar P., Zoete V., Röhrig U.F., 2017. Journal of Chemical Information and Modeling, 57 (1) pp. 73-84. Peer-reviewed.
 
The Binding Mode of N-Hydroxyamidines to Indoleamine 2,3-Dioxygenase 1 (IDO1).
Röhrig U.F., Zoete V., Michielin O., 2017. Biochemistry, 56 (33) pp. 4323-4325. Peer-reviewed.
 
1,2,3-Triazoles as inhibitors of indoleamine 2,3-dioxygenase 2 (IDO2).
Röhrig U.F., Majjigapu S.R., Caldelari D., Dilek N., Reichenbach P., Ascencao K., Irving M., Coukos G., Vogel P., Zoete V. et al., 2016/09/01. Bioorganic & medicinal chemistry letters, 26 (17) pp. 4330-4333. Peer-reviewed.
Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape.
Zoete V., Schuepbach T., Bovigny C., Chaskar P., Daina A., Röhrig U.F., Michielin O., 2016. Journal of Computational Chemistry, 37 (4) pp. 437-447. Peer-reviewed.
Proteolysis of HCF-1 by Ser/Thr glycosylation-incompetent O-GlcNAc transferase:UDP-GlcNAc complexes.
Kapuria V., Röhrig U.F., Bhuiyan T., Borodkin V.S., van Aalten D.M., Zoete V., Herr W., 2016. Genes and Development, 30 (8) pp. 960-972. Peer-reviewed.
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.
SIB Swiss Institute of Bioinformatics Members, 2016. Nucleic Acids Research, 44 (D1) pp. D27-D37.
 
Challenges in the Discovery of Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors.
Röhrig U.F., Majjigapu S.R., Vogel P., Zoete V., Michielin O., 2015. Journal of Medicinal Chemistry, 58 (24) pp. 9421-9437. Peer-reviewed.
 
Single amino acid charge switch defines clinically distinct proline-serine-threonine phosphatase-interacting protein 1 (PSTPIP1)-associated inflammatory diseases.
Holzinger D., Fassl S.K., de Jager W., Lohse P., Röhrig U.F., Gattorno M., Omenetti A., Chiesa S., Schena F., Austermann J. et al., 2015. Journal of Allergy and Clinical Immunology, 136 (5) pp. 1337-1345. Peer-reviewed.
 
Detailed analysis and follow-up studies of a high-throughput screening for indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors.
Röhrig U.F., Majjigapu S.R., Chambon M., Bron S., Pilotte L., Colau D., Van den Eynde B.J., Turcatti G., Vogel P., Zoete V. et al., 2014. European Journal of Medicinal Chemistry, 84 pp. 284-301.
 
Origin of the spectral shifts among the early intermediates of the rhodopsin photocycle.
Campomanes P., Neri M., Horta B.A., Röhrig U.F., Vanni S., Tavernelli I., Rothlisberger U., 2014. Journal of the American Chemical Society, 136 (10) pp. 3842-3851.
 
Toward on-the-fly quantum mechanical/molecular mechanical (QM/MM) docking: development and benchmark of a scoring function.
Chaskar P., Zoete V., Röhrig U.F., 2014. Journal of Chemical Information and Modeling, 54 (11) pp. 3137-3152. Peer-reviewed.
 
Rational design of 4-aryl-1,2,3-triazoles for indoleamine 2,3-dioxygenase 1 inhibition.
Röhrig U.F., Majjigapu S.R., Grosdidier A., Bron S., Stroobant V., Pilotte L., Colau D., Vogel P., Van den Eynde B.J., Zoete V. et al., 2012. Journal of Medicinal Chemistry, 55 (11) pp. 5270-5290. Peer-reviewed.
Molecular mechanism of a green-shifted, pH-dependent red fluorescent protein mKate variant.
Wang Q., Byrnes L.J., Shui B., Röhrig U.F., Singh A., Chudakov D.M., Lukyanov S., Zipfel W.R., Kotlikoff M.I., Sondermann H., 2011. PLoS One, 6 (8) pp. e23513. Peer-reviewed.
 
Structure-function analyses point to a polynucleotide-accommodating groove essential for APOBEC3A restriction activities.
Bulliard Y., Narvaiza I., Bertero A., Peddi S., Röhrig U.F., Ortiz M., Zoete V., Castro-Díaz N., Turelli P., Telenti A. et al., 2011. Journal of Virology, 85 (4) pp. 1765-1776.
Frequent MAGE mutations in human melanoma.
Caballero O.L., Zhao Q., Rimoldi D., Stevenson B.J., Svobodová S., Devalle S., Röhrig U.F., Pagotto A., Michielin O., Speiser D. et al., 2010. PLoS One, 5 (9) pp. e12773.
 
Rational design of indoleamine 2,3-dioxygenase inhibitors.
Röhrig U.F., Awad L., Grosdidier A., Larrieu P., Stroobant V., Colau D., Cerundolo V., Simpson A.J., Vogel P., Van den Eynde B.J. et al., 2010. Journal of Medicinal Chemistry, 53 (3) pp. 1172-1189.
 
Docking to heme proteins.
Röhrig U.F., Grosdidier A., Zoete V., Michielin O., 2009. Journal of Computational Chemistry, 30 (14) pp. 2305-2315.
 
Functional analysis and structural modeling of human APOBEC3G reveal the role of evolutionarily conserved elements in the inhibition of human immunodeficiency virus type 1 infection and Alu transposition.
Bulliard Y., Turelli P., Röhrig U.F., Zoete V., Mangeat B., Michielin O., Trono D., 2009. Journal of Virology, 83 (23) pp. 12611-12621.
 
Molecular Modeling of Proteins: From Simulations to Drug Design Applications
Zoete V., Cuendet M, Röhrig U.F., Grosdidier A., Michielin O., 2009. pp. 247-281 dans Appel R.D., Feytmans E. (eds.) Bioinformatics: s swiss perspective, World Scientific.
 
NMR chemical shifts of the rhodopsin chromophore in the dark state and in bathorhodopsin: a hybrid QM/MM molecular dynamics study.
Röhrig U.F., Sebastiani D., 2008. Journal of Physical Chemistry. B, 112 (4) pp. 1267-1274. Peer-reviewed.
 
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.
Montero-Cabrera L.A., Röhrig U., Padrón-Garcia J.A., Crespo-Otero R., Montero-Alejo A.L., Garcia de la Vega J.M., Chergui M., Rothlisberger U., 2007. Journal of Chemical Physics, 127 (14) p. 145102. Peer-reviewed.
 
In Silico Dynamic Studies of Cis-Trans Isomerization in Organic and Biological Systems
Röhrig U.F., Tavernelli I., Rothlisberger U., 2006. pp. 113-141 dans Dugave C. (eds.) cis-trans Isomerization in Biochemistry chap. 7, Wiley-VCH.
 
Stability and structure of oligomers of the Alzheimer peptide Abeta16-22: from the dimer to the 32-mer.
Röhrig U.F., Laio A., Tantalo N., Parrinello M., Petronzio R., 2006. Biophysical Journal, 91 (9) pp. 3217-3229. Peer-reviewed.
 
Molecular dynamics in electronically excited states using time-dependent density functional theory
Tavernelli I., Röhrig U.F., Rothlisberger U., 2005. Molecular Physics, 103 (6-8) pp. 963-981. Peer-reviewed.
 
Optical properties of molecules in solution via hybrid TDDFT/MM simulations
Sulpizi M., Röhrig U.F., Hutter J., Rothlisberger U., 2005. International Journal of Quantum Chemistry, 101 (6) pp. 671-682. Peer-reviewed.
 
QM/MM simulation of the first step of vision
Röhrig U.F., Grimm S., Frank I., Guidoni L., Laio A., Rothlisberger U., 2005. pp. 237-243 dans Wagner S., Hanke W., Bode A., Durst F. (eds.) High performance computing in science and engineering, Munich 2004, Springer.
 
Quantum mechanical/molecular mechanical (OM/MM) car-parrinello Simulations in excited states
Moret M.E., Tapavicza E., Guidoni L, Röhrig U.F., Sulpizi Marialore, Tavernelli Ivano, Rothlisberger Ursula, 2005. CHIMIA, 59 (7) pp. 493-498.
 
Solvent and protein effects on the structure and dynamics of the rhodopsin chromophore.
Röhrig U.F., Guidoni L., Rothlisberger U., 2005. ChemPhysChem, 6 (9) pp. 1836-1847. Peer-reviewed.
 
A molecular spring for vision.
Röhrig U.F., Guidoni L., Laio A., Frank I., Rothlisberger U., 2004. Journal of the American Chemical Society, 126 (47) pp. 15328-15329. Peer-reviewed.
 
Organic chromophores under tensile stress
Röhrig U.F., Troppmann U., Frank I., 2003. Chemical Physics, 289 (2-3) pp. 381-388. Peer-reviewed.
 
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.
Röhrig U.F., Frank I., Hutter J., Laio A., VandeVondele J., Rothlisberger U., 2003. ChemPhysChem, 4 (11) pp. 1177-1182. Peer-reviewed.
 
Early steps of the intramolecular signal transduction in rhodopsin explored by molecular dynamics simulations.
Röhrig U.F., Guidoni L., Rothlisberger U., 2002. Biochemistry, 41 (35) pp. 10799-10809. Peer-reviewed.
 
Hybrid QM/MM Car-Parrinello Simulations of Catalytic and Enzymatic Reactions
Colombo M.C., Guidoni L., Laio A., Magistrato A., Maurer P., Piana S., Röhrig U.F., Spiegel K., Sulpizi M., VandeVondele J. et al., 2002. CHIMIA, 56 (1) pp. 13-19.
 
First-principles molecular dynamics study of a polymer under tensile stress
Röhrig U.F., Frank I., 2001. Journal of Chemical Physics, 115 (18) p. 8670. Peer-reviewed.
 
Syntheses of phosphinine-based tripodal ligands
Röhrig U.F., Mézailles N., Maigrot N., Ricard L., Mathey F., Le Floch P., 2000. European Journal of Inorganic Chemistry, 2000 (12) pp. 2565-2571. Peer-reviewed.
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