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The PMF platform just started, and publications mentioning it will be released soon.

In the meantime, here is a list of publications of the SIB Molecular Modeling group illustrating some of the technologies and expertise provided by the PMF :


Röhrig UF, Majjigapu SR, Grosdidier A, Bron S, Stroobant V, Pilotte L, Colau D, Vogel P, Van den Eynde BJ, Zoete V, Michielin O
Rational Design of 4-Aryl-1,2,3-Triazoles for Indoleamine 2,3-Dioxygenase 1 Inhibition.
J. Med. Chem., 2012, minor revision.

Gfeller D, Michielin O, Zoete V.
Expanding molecular modeling and design tools to non-natural sidechains.
J Comput Chem. 2012, in print.

Baitsch L, Legat A, Barba L, Fuertes Marraco SA, Rivals JP, Baumgaertner P, Christiansen-Jucht C, Bouzourene H, Rimoldi D, Pircher H, Rufer N, Matter M, Michielin O, Speiser DE.
Extended co-expression of inhibitory receptors by human CD8 T-cells depending on differentiation, antigen-specificity and anatomical localization.
PLoS One., 2012, 7, e30852.

Baumgaertner P, Jandus C, Rivals JP, Derré L, Lövgren T, Baitsch L, Guillaume P, Luescher IF, Berthod G, Matter M, Rufer N, Michielin O, Speiser DE.
Vaccination-induced functional competence of circulating human tumor-specific CD8 T-cells.
Int J Cancer., 2012, 130, 2607-17.

von Moos R, Seifert B, Simcock M, Goldinger SM, Gillessen S, Ochsenbein A, Michielin O, Cathomas R, Schläppi M, Moch H, Schraml PH, Mjhic-Probst D, Mamot C, Schönewolf N, Dummer R; Swiss Group for Clinical Cancer Research (SAKK).
First-line temozolomide combined with bevacizumab in metastatic melanoma: a multicentre phase II trial (SAKK 50/07).
Ann Oncol., 2012, 23, 531-6.



Nikolaev SI, Rimoldi D, Iseli C, Valsesia A, Robyr D, Gehrig C, Harshman K, Guipponi M, Bukach O, Zoete V, Michielin O, Muehlethaler K, Speiser D, Beckmann JS, Xenarios I, Halazonetis TD, Jongeneel CV, Stevenson BJ, Antonarakis SE.
Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma.
Nat Genet., 2011, 44, 133-9.

Grosdidier A, Zoete V, Michielin O.
SwissDock, a protein-small molecule docking web service based on EADock DSS.
Nucleic Acids Res., 2011, 39(Web Server issue), W270-7.

Grosdidier A, Zoete V, Michielin O.
Fast docking using the CHARMM force field with EADock DSS.
J Comput Chem., 2011, 32, 2149–2159.

Zoete V, Cuendet MA, Grosdidier A, Michielin O.
SwissParam: a fast force field generation tool for small organic molecules.
J Comput Chem., 2011, 32, 2359-68.

Cuendet MA, Zoete V, Michielin O.
How T cell receptors interact with peptide-MHCs: a multiple steered molecular dynamics study.
Proteins., 2011, 79, 3007-24.

Leimgruber A, Ferber M, Irving M, Hussain-Kahn H, Wieckowski S, Derré L, Rufer N, Zoete V, Michielin O.
TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires.
PLoS One., 2011, 6, e26301.

Speiser DE, Wieckowski S, Gupta B, Iancu EM, Baumgaertner P, Baitsch L, Michielin O, Romero P, Rufer N.
Single cell analysis reveals similar functional competence of dominant and nondominant CD8 T-cell clonotypes.
Proc Natl Acad Sci U S A., 2011, 108, 15318-23.

Rahm N, Yap M, Snoeck J, Zoete V, Muñoz M, Radespiel U, Zimmermann E, Michielin O, Stoye JP, Ciuffi A, Telenti A.
Unique spectrum of activity of prosimian TRIM5alpha against exogenous and endogenous retroviruses.
J Virol., 2011, 85, 4173-83.

Maillard PV, Zoete V, Michielin O, Trono D.
Homology-based identification of capsid determinants that protect HIV1 from human TRIM5α restriction.
J Biol Chem., 2011, 286, 8128-40.

Sala E, Guasch L, Iwaszkiewicz J, Mulero M, Salvadó MJ, Bladé C, Ceballos M, Valls C, Zoete V, Grosdidier A, Garcia-Vallvé S, Michielin O, Pujadas G.
Identification of human IKK-2 inhibitors of natural origin (Part II): in Silico prediction of IKK-2 inhibitors in natural extracts with known anti-inflammatory activity.
Eur J Med Chem., 2011, 46, 6098-103.

Strasser B, Iwaszkiewicz J, Michielin O, Mayer A.
The V-ATPase proteolipid cylinder promotes the lipid-mixing stage of SNARE-dependent fusion of yeast vacuoles.
EMBO J., 2011, 30, 4126-41.

Berthod G, Homicsko K, Bouchaab H, Matter M, Cerottini JP, Guggisberg D, Speiser D, Leyvraz S, Michielin O.
Melanoma: a new therapeutic era.
Rev Med Suisse., 2011, 7, 1126-30.

Sala E, Guasch L, Iwaszkiewicz J, Mulero M, Salvadó MJ, Pinent M, Zoete V, Grosdidier A, Garcia-Vallvé S, Michielin O, Pujadas G.
Identification of human IKK-2 inhibitors of natural origin (part I): modeling of the IKK-2 kinase domain, virtual screening and activity assays.
PLoS One., 2011, 6, e16903. 



Röhrig UF, Awad L, Grosdidier A, Larrieu P, Stroobant V, Colau D, Cerundolo V, Simpson AJ, Vogel P, Van den Eynde BJ, Zoete V, Michielin O.
Rational Design of Indoleamine 2,3-Dioxygenase Inhibitors.
J Med Chem., 2010, 53, 1172-89.

Zoete V, Grosdidier A, Cuendet M, Michielin O
Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.
J Mol Recognit., 2010, 23, 457-61.

Schupbach T, Zoete V, Tsakam-Sotche B, Michielin O.
Fourier transform convolution integrals applied to generalized Born molecular volume.
J Comput Chem, 2010, 31, 649-59.

Zoete V, Irving MB, Michielin O.
MM-GBSA binding free energy decomposition and T cell Receptor engineering.
J Mol. Recognition, 2010, 23, 142-52.

Bulliard Y, Narvaiza I, Bertero A, Peddi S, Röhrig UF, Ortiz M, Zoete V, Castro-Díaz N, Turelli P, Telenti A, Michielin O, Weitzman MD, Trono D.
Structure-Function Analyses Point to a Polynucleotide-Accommodating Groove Essential for APOBEC3A Restriction Activities.
J Virol. 2010, 85,1765-76.

Maillard PV, Zoete V, Michielin O, Trono D.
Homology-based identification of capsid determinants that protect HIV1 from human TRIM5{alpha} restriction.
J Biol Chem. 2010, in press.

Liechti LA, Bernèche S, Bargeton B, Iwaszkiewicz J, Roy S, Michielin O, Kellenberger S.
A combined computational and functional approach identifies new residues involved in pH-dependent gating of ASIC1a.
J Biol Chem. 2010, 285, 16315-29.

Caballero OL, Zhao Q, Rimoldi D, Stevenson BJ, Svobodová S, Devalle S, Röhrig UF, Pagotto A, Michielin O, Speiser D, Wolchok JD, Liu C, Pejovic T, Odunsi K, Brasseur F, Van den Eynde BJ, Old LJ, Lu X, Cebon J, Strausberg RL, Simpson AJ.
Frequent MAGE mutations in human melanoma.
PLoS One. 2010, 5, pii: e12773.

Derré L, Rivals JP, Jandus C, Pastor S, Rimoldi D, Romero P, Michielin O, Olive D, Speiser DE.
BTLA mediates inhibition of human tumor-specific CD8+ T cells that can be partially reversed by vaccination.
J Clin Invest., 2010, 120, 157-67.

Schmid DA, Irving MB, Posevitz V, Hebeisen M, Posevitz-Fejfar A, Sarria JC, Gomez-Eerland R, Thome M, Schumacher TN, Romero P, Speiser DE, Zoete V, Michielin O, Rufer N.
Evidence for a TCR affinity threshold delimiting maximal CD8 T cell function.
J Immunol. 2010, 184, 4936-46.

Bizzini A, Entenza JM, Michielin O, Arnold I, Erni B, Moreillon P.
A single mutation in enzyme I of the sugar phosphotransferase system confers penicillin tolerance to Streptococcus gordonii.
Antimicrob Agents Chemother., 2010, 54, 259-66.



Röhrig, U. F., Grosdidier, A., Zoete, V. & Michielin, O.
Docking to heme proteins.
J Comput Chem, 2009, 30, 2305-2315.

Grosdidier A, Zoete, V, Michielin O.
Blind docking of 260 protein-ligand complexes with EADock 2.0.
J Comput Chem, 2009, 30, 2021-2030.

Zoete V, Grosdidier A, Michielin O.
Docking, virtual high throughput screening and in silico fragment-based drug design.
J Cell Mol Med, 2009, 13, 238-48.

Bulliard Y, Turelli P, Rohrig UF, Zoete V, Mangeat B, Michielin O, Trono D.
Functional Analysis and Structural Modeling of Human APOBEC3G Reveals the Role of Evolutionarily Conserved Elements in HIV-1 and Alu Inhibition.
J Virol, 2009, 83, 12611-21.

Hornitschek P, Lorrain S, Zoete V, Michielin O, Fankhauser C.
HFR1 inhibits the shade avoidance response by heterodimerizing with elongation growth promoting bHLH class transcription factors.
EMBO J, 2009, 28, 3893-902.

Prior JO, Montemurro M, Orcurto MV, Michielin O, Luthi F, Benhattar J, Guillou L, Elsig V, Stupp R, Delaloye AB, Leyvraz S.
Early prediction of response to sunitinib after imatinib failure by 18F-fluorodeoxyglucose positron emission tomography in patients with gastrointestinal stromal tumor.
J Clin Oncol, 2009, 27, 439-445.



Michielin O, Rufer N, Romero P, Laurent J, Cerottini JP, Gugisberg D, Leyvraz S, Speiser DE.
New developments in cancer immunotherapy.
Rev Med Suisse, 2008, 4, 1248-1251.

Capendeguy O, Iwaszkiewicz J, Michielin O, Horisberger JD
The fourth extracellular loop of the alpha subunit of Na,K-ATPase. Functional evidence for close proximity with the second extracellular loop.
J Biol Chem, 2008, 283, 27850- 27858.

Chodanowski P, Grosdidier A, Feytmans E, Michielin O
Local alignment refinement using structural assessment.
PLoS ONE, 2008, 3, e2645.

Cuendet MA, Michielin O
Protein-Protein Interaction Investigated by Steered Molecular Dynamics: the TCR-pMHC Complex.
Biophys J, 2008, 95, 3575-3590.

Rochat B, Zoete V, Grosdidier A, von Grunigen S, Marull M, Michielin O.
In vitro biotransformation of imatinib by the tumor expressed CYP1A1 and CYP1B1.
Biopharm Drug Dispos 29, 103-118 (2008).

Derre L, Bruyninx M, Baumgaertner P, Ferber M, Schmid D, Leimgruber A, Zoete V, Romero P, Michielin O, Speiser DE, Rufer N.
Distinct sets of alphabeta TCRs confer similar recognition of tumor antigen NY-ESO-1157-165 by interacting with its central Met/Trp residues.
Proc Natl Acad Sci U S A, 2008, 105, 15010-15015.

Voelter V, Rufer N, Reynard S, Greub G, Brookes R, Guillaume P, Grosjean F, Fagerberg T, Michielin O, Rowland-Jones S, Pinilla C, Leyvraz S, Romero P, Appay V.
Characterization of Melan-A reactive memory CD8+ T cells in a healthy donor.
Int Immunol 20, 1087-1096 (2008).



Derré L, Ferber M, Touvrey C, Devevre E, Zoete V, Leimgruber A, Romero P, Michielin O, Lévy F, Speiser DE.
A novel population of human melanoma-specific CD8 T cells recognizes Melan-AMART-1 immunodominant nonapeptide but not the corresponding decapeptide.
J Immunol., 2007 Dec 1;179(11):7635-45.

Stupp R, Pica A, Mirimanoff RO, Michielin O.
A practical guide for the management of gliomas
Bull Cancer., 2007, 94(9), 817-22

Michielin O.
Application of molecular modelling to new therapeutic cancer approaches
Bull Cancer. 2007 Sep 1;94(9):763-8

Feige JN, Gelman L, Rossi D, Zoete V, Metivier R, Tudor C, Anghel SI, Grosdidier A, Lathion C, Engelborghs Y, Michielin O, Wahli W, Desvergne B.
The endocrine disruptor mono-ethyl-hexyl-phthalate is a selective PPARgamma modulator which promotes adipogenesis
J Biol Chem, 2007, 282(26), 19152-66

Alves PM, Viatte S, Fagerberg T, Michielin O, Bricard G, Bouzourene H, Vuilleumier H, Kruger T, Givel JC, Lévy F, Speiser DE, Cerottini JC, Romero P.
Immunogenicity of the carcinoembryonic antigen derived peptide 694 in HLA-A2 healthy donors and colorectal carcinoma patients
Cancer Immunol. Immunother., 2007, 56(11), 1795-805

Zhang KL, Mangeat B, Ortiz M, Zoete V, Trono D, Telenti A, Michielin O.
Model Structure of Human APOBEC3G
PLoS ONE., 2007, 2(4), e378

Zoete V, Grosdidier A, Michielin O.
Peroxisome proliferator-activated receptor structures: Ligand specificity, molecular switch and interactions with regulators
Biochim. Biophys. Acta, 2007, 1771(8), 915-25

Grosdidier A, Zoete V, Michielin O.
EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization
Proteins, 2007, 67(4): 1010-25

Zoete V, Michielin O.
Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: application to the TCR-p-MHC complex
Proteins, 2007, 67(4): 1026-47

Michalik L, Zoete V, Krey G, Grosdidier A, Gelman L, Chodanowski P, Feige JN, Desvergne B, Wahli W, Michielin O.
Combined simulation and mutagenesis analyses reveal the involvement of key residues for peroxisome proliferator-activated receptor alpha helix 12 dynamic behavior
J. Biol. Chem., 2007, 282(13): 9666-77

Butticaz C, Michielin O, Wyniger J, Telenti A, Rothenberger S.
Silencing of both beta-TrCP1 and HOS (beta-TrCP2) is required to suppress human immunodeficiency virus type 1 Vpu-mediated CD4 down-modulation
J. Virol., 2007, 81(3): 1502-5



Colombetti S, Fagerberg T, Baumgartner P, Chapatte L, Speiser DE, Rufer N, Michielin O, Levy F
Impact of orthologous Melan-A peptide immunizations on the anti-self Melan-A/HLA-A2 T cell cross-reactivity
J Immunology, 2006, 176 (11): 6560-6567

Aublin A, Ciofani M, Willkomm N, Hamrouni A, Szymczak-Workman AL, Takahashi T, Sandjeu Y, Guillaume P, Vignali DA, Michielin O, Zúñiga-Pflücker JC, Maryanski JL.
A natural structural variant of the mouse TCR beta-chain displays intrinsic receptor function and antigen specificity
J Immunology, 2006, 177 (12): 8587-8594

Yip YL, Zoete V, Scheib H, Michielin O
Structural assessment of single amino acid mutations: Application to TP53 function
Human Mutation, 2006, 27(9): 926-937

Capendeguy O, Chodanowski P, Michielin O, Horisberger JD
Access of extracellular cations to their binding sites in Na, K-ATPase: Role of the second extracellular loop of the alpha subunit
J Gen Physiol, 2006, 127(3): 341-352

Fagerberg T, Cerottini JC, Michielin O
Structural prediction of peptides bound to MHC class I
J Mol Biol, 2006, 356(2): 521-46

Koch M, Schmid F, Zoete V, Meuwly M
Insulin: a model system for nanomedicine? Nanomedicine,
2006, 1(3): 373-8

Zoete V, Meuwly M
Importance of individual side chains for the stability of a protein fold: Computational alanine scanning of the insulin monomer
J Comput Chem, 2006, 27(15): 1843-57

Thorsteinsdottir HB, Schwede T, Zoete V, Meuwly M
How inaccuracies in protein structure models affect estimates of protein-ligand interactions: Computational analysis of HIV-1 protease inhibitor binding
Proteins, 2006, 65(2): 407-23



Suarez M, Haenni M, Canarelli S, Fisch F, Chodanowski P, Servis C, Michielin O, Freitag R, Moreillon P, Mermod N. Structure-function characterization and optimization of a plant-derived antibacterial peptide Antimicrob Agents Chemother. 2005, 49(9): 3847-57

De Los Rios P, Cecconi F, Pretre A, Dietler G, Michielin O, Piazza F, Juanico B. Functional dynamics of PDZ binding domains: a normal-mode analysis. Biophys J, 2005, 89(1): 14-21

Michielin O, Blanchet JS, Fagerberg T, Valmori D, Rubio-Godoy V, Speiser D, Ayyoub M, Alves P, Luescher I, Gairin JE, Cerottini JC, Romero P. Tinkering with nature: the tale of optimizing peptide based cancer vaccines Cancer Treat Res, 2005,123: 267-91

Filges I, Zaman K, Michielin O, Vulliémoz D, Perey L, Stupp R. Present chemoprevention and future vision Rev Med Suisse, 2005, 1(20):1343-6, 1349

Cebecauer M, Guillaume P, Mark S, Michielin O, Boucheron N, Bezard M, Meyer BH, Segura JM, Vogel H, Luescher IF. CD8+ cytotoxic T lymphocyte activation by soluble major histocompatibility complex-peptide dimmers J Biol Chem, 2005, 280(25): 23820-8



Li C, Grosdidier A, Crambert G, Horisberger JD, Michielin O, Geering K. Structural and functional interaction sites between Na,K-ATPase and FXYD proteins J Biol Chem, 2004, 279(37): 38895-902

Hauert J, Fernandez-Carneado J, Michielin O, Mathieu S, Grell D, Schapira M, Spertini O, Mutter M, Tuchscherer G, Kovacsovics T. A template-assembled synthetic protein surface mimetic of the von Willebrand factor A1 domain inhibits botrocetin-induced platelet aggregation Chembiochem, 2004, 5(6): 856-64

Horisberger JD, Kharoubi-Hess S, Guennoun S, Michielin O. The fourth transmembrane segment of the Na,K-ATPase alpha subunit: a systematic mutagenesis study J Biol Chem, 2004, 279(28): 29542-50



Schwitzgebel VM, Mamin A, Brun T, Ritz-Laser B, Zaiko M, Maret A, Jornayvaz FR, Theintz GE, Michielin O, Melloul D, Philippe J. Agenesis of human pancreas due to decreased half-life of insulin promoter factor 1 J Clin Endocrinol Metab, 2003, 88(9): 4398-406

Dietrich PY, Le Gal FA, Dutoit V, Pittet MJ, Trautman L, Zippelius A, Cognet I, Widmer V, Walker PR, Michielin O, Guillaume P, Connerotte T, Jotereau F, Coulie PG, Romero P, Cerottini JC, Bonneville M, Valmori D. Prevalent role of TCR alpha-chain in the selection of the preimmune repertoire specific for a human tumor-associated self-antigen J Immunol, 2003, 170(10): 5103-9

Bernimoulin MP, Zeng XL, Abbal C, Giraud S, Martinez M, Michielin O, Schapira M, Spertini O. Molecular basis of leukocyte rolling on PSGL-1. Predominant role of core-2 O-glycans and of tyrosine sulfate residue 51 J Biol Chem, 2003, 278(1): 37-47

Doucey MA, Goffin L, Naeher D, Michielin O, Baumgärtner P, Guillaume P, Palmer E, Luescher IF. CD3 delta establishes a functional link between the T cell receptor and CD8 J Biol Chem, 2003, 278(5): 3257-64

Zoete V, Michielin O, Karplus M. Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors J Comput Aided Mol Des, 2003, 17(12): 861-80



Zoete V, Michielin O, Karplus M. Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility J Mol Biol, 2002, 315(1): 21-52

Michielin O, Karplus M. Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis J Mol Biol, 2002, 324(3): 547-69

Romero P, Valmori D, Pittet MJ, Zippelius A, Rimoldi D, Lévy F, Dutoit V, Ayyoub M, Rubio-Godoy V, Michielin O, Guillaume P, Batard P, Luescher IF, Lejeune F, Liénard D, Rufer N, Dietrich PY, Speiser DE, Cerottini JC. Antigenicity and immunogenicity of Melan-A/MART-1 derived peptides as targets for tumor reactive CTL in human melanoma Immunol Rev, 2002, 188: 81-96

Michielin O, Zoete V, Gierasch TM, Eckstein J, Napper A, Verdine G, Karplus M. Conformational analysis of a stereochemically complete set of cis-enediol peptide analogues J Am Chem Soc, 2002, 124(37): 11131-41