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Department of Biochemistry

Publications Caflisch Group since 2010


Bedi, RK., Huang, D., Li, Y. & Caflisch, A. Structure-Based Design of Inhibitors of the m6 A-RNA Writer Enzyme METTL3. ACS Bio Med Chem Au 3, 359-370 (2023). PMID: 37599794.

Bobrovs, R., Drunka, L., Kanepe, I., Jirgensons, A., Caflisch, A., Salvalaglio, M. & Jaudzems, K. Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors. J Chem Inf Model [Epub ahead of print] (2023). PMID: 37801405.

Cazzanelli, G., Vedove, AD., Parolin, E., D'Agostino, VG., Unzue, A., Nevado, C., Caflisch, A. & Lolli, G. Reevaluation of bromodomain ligands targeting BAZ2A. Protein Sci 32, e4752 (2023). PMID:

Ilie, IM., Ehrhardt, C., Caflisch, A. & Weitz-Schmidt, G. Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations. J Chem Inf Model 63, 3878-3891 (2023). PMID: 37310029.

Reimann, RR., Puzio, M., Rosati, A., Emmenegger, M., Schneider, BL., Valdés, P., Huang, D., Caflisch, A. & Aguzzi, A. Rapid ex vivo reverse genetics identifies the essential determinants of prion protein toxicity. Brain Pathol 33, e13130  (2023). PMID: 36329611.

Vargas-Rosales, PA., D'Addio, A., Zhang, Y. & Caflisch, A. Disrupting Dimeric β-Amyloid by Electric Fields. ACS Phys Chem Au 3, 456-466 (2023). PMID: 37780539.

Widmer, J., Langini, C., Vitalis, A. & Caflisch, A. Optimized reaction coordinates for analysis of enhanced sampling. J Chem Phys 159, (2023). PMID: 37403854.

Xiang, Y., Zhai, G., Li, Y., Wang, M., Chen, X., Wang, R., Xie, H., Zhang, W., Ge, G., Zhang, Q., Xu, Y., Caflisch, A., Xu, J., Chen, H. & Chen, L. Ginkgolic acids inhibit SARS-CoV-2 and its variants by blocking the spike protein/ACE2 interplay. Int J Biol Macromol 226, 780-792 (2023). PMID: 36521705.


Cocina, F., Vitalis, A. & Caflisch, A. Spiking burstiness and working memory in the human medial temporal lobe. Cereb Cortex Commun 3, tgac039 (2022). PMID: 36415307.

Dalle Vedove, A., Cazzanelli, G., Batiste, L., Marchand, JR., Spiliotopoulos, D., Corsi, J., D'Agostino, VG., Caflisch, A. & Lolli, G. Identification of a BAZ2A-Bromodomain Hit Compound by Fragment Growing. ACS Med Chem Lett 13, 1434-1443 (2022). PMID: 36105334.

Dehabadi, MH., Caflisch, A., Ilie, IM. & Firouzi, R. 42 Dimer: A Computational Study. J Phys Chem B 126, 7627-7637 (2022). PMID: 36148988.

García-Viñuales, S., Ilie, IM., Santoro, AM., Romanucci, V., Zarrelli, A., Di Fabio, G., Caflisch, A. & Milardi, D. Silybins inhibit human IAPP amyloid growth and toxicity through stereospecific interactions. Biochim Biophys Acta Proteins Proteom 1870, 140772 (2022). PMID: 35307557.

Giordano, D., Langini, C., Caflisch, A., Marabotti, A. & Facchiano, A. Streptomyces mobaraensis. Comput Struct Biotechnol J 20, 3924-3934 (2022). PMID: 35950183.

Ilie, IM. & Caflisch, A. Antibody binding increases the flexibility of the prion protein. Biochim Biophys Acta Proteins Proteom 1870, 140827 (2022). PMID: 35931365.

Ilie, IM., Bacci, M., Vitalis, A. & Caflisch, A. Antibody binding modulates the dynamics of the membrane bound prion protein. Biophys J 121, 2813-2825 (2022). PMID: 35672948.

Nai, F., Nachawati, R., Zálešák, F., Wang, X., Li, Y. & Caflisch, A. 6A-RNA Reader YTHDF2. ACS Med Chem Lett 13, 1500-1509 (2022). PMID: 36110386.

Nass, KJ., Ilie, IM., Saller, MJ., Driessen, AJM., Caflisch, A., Kammerer, RA. & Li, X. The role of the N-terminal amphipathic helix (N-AH) in bacterial YidC: Insights from functional studies, the crystal structure and molecular dynamics simulations. Biochim Biophys Acta Biomembr 1864, 183825 (2022). PMID: 34871574

Salutari, I. & Caflisch, A. Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein. J Chem Inf Model 62, 1014-1024 (2022). PMID: 35119862.

Schilling, J., Jost, C., Ilie, IM., Schnabl, J., Buechi, O., Eapen, RS., Truffer, R., Caflisch, A. & Forrer, P. Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. J Biol Chem 298(1), 101403 (2022). PMID: 34793836.

Andrés Vargas-Rosales, P. & Caflisch, A. Domino effect in allosteric signaling of peptide binding. J Mol Biol 434, 167661 (2022). PMID: 35640719.

Cappelletti, V., Hauser, T., Piazza, I., Pepelnjak, M., Malinovska, L., Fuhrer, T., Li, Y., Dörig, C., Boersema, P., Gillet, L., Grossbach, J., Dugourd, A., Saez-Rodriguez, J., Beyer, A., Zamboni, N., Caflisch, A., de Souza, N. & Picotti, P. Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell 184, 545-559.e22 (2021). PMID: 33357446.

Cocina, F., Vitalis, A. & Caflisch, A. Unsupervised methods for detection of neural states: case study of hippocampal-amygdala interactions. eNeuro 8, (2021). PMID: 34544761.

Dolbois, A., Bedi, RK., Bochenkova, E., Müller, A., Moroz-Omori, EV., Huang, D. & Caflisch, A. 1,4,9-Triazaspiro[5.5]undecan-2-one Derivatives as Potent and Selective METTL3 Inhibitors. J Med Chem 64, 12738-12760 (2021). PMID: 34431664.

Dalle Vedove, A., Cazzanelli, G., Corsi, J., Sedykh, M., D'Agostino, V.G., Caflisch, A., Lolli, G. Identification of a BAZ2A bromodomain hit compound by fragment joining.  ACS Bio Med Chem Au (2021)

Lee, JH., Wang, R., Xiong, F., Krakowiak, J., Liao, Z., Nguyen, PT., Moroz-Omori, EV., Shao, J., Zhu, X., Bolt, MJ., Wu, H., Singh, PK., Bi, M., Shi, CJ., Jamal, N., Li, G., Mistry, R., Jung, SY., Tsai, KL., Ferreon, JC., Stossi, F., Caflisch, A., Liu, Z., Mancini, MA. & Li, W. Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. Mol Cell 81, 3368-3385.e9 (2021). PMID: 34375583.

Li, Y., Bedi, RK., Wiedmer, L., Sun, X., Huang, D. & Caflisch, A. 6A) Recognition by the Reader Domain of YTHDC1. J Chem Theory Comput 17, 1240-1249 (2021). PMID: 33472367.

Mallona, I., Ilie, IM., Karemaker, ID., Butz, S., Manzo, M., Caflisch, A. & Baubec, T. Flanking sequence preference modulates de novo DNA methylation in the mouse genome. Nucleic Acids Res 49, 145-157 (2021). PMID: 33290556.

Milardi, D., Gazit, E., Radford, SE., Xu, Y., Gallardo, RU., Caflisch, A., Westermark, GT., Westermark, P., Rosa, C. & Ramamoorthy, A. Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes. Chem Rev 121, 1845-1893 (2021). PMID: 33427465.

Moroz-Omori, EV., Huang, D., Bedi, RK., Cheriyamkunnel, SJ., Bochenkova, E., Dolbois, A., Rzeczkowski, MD., Li, Y., Wiedmer, L. & Caflisch, A. METTL3 inhibitors for epitranscriptomic modulation of cellular processes. ChemMedChem 16, 3035-3043 (2021). PMID: 34237194

Pohl, MO., Busnadiego, I., Marrafino, F., Wiedmer, L., Hunziker, A., Fernbach, S., Glas, I., Moroz-Omori, EV., Hale, BG., Caflisch, A. & Stertz, S. Combined computational and cellular screening identifies synergistic inhibition of SARS-CoV-2 by lenvatinib and remdesivir. J Gen Virol 102, (2021). PMID: 34319869.

Bedi, RK., Huang, D., Eberle, SA., Wiedmer, L., Śledź, P. & Caflisch, A. Small-Molecule Inhibitors of METTL3, the Major Human Epitranscriptomic Writer. ChemMedChem 15, 744-748 (2020). PMID: 32159918.

Bedi, RK., Huang, D., Wiedmer, L., Li, Y., Dolbois, A., Wojdyla, JA., Sharpe, ME., Caflisch, A. & Sledz, P. 6A-Dependent Protein-RNA Interactions with Fragments. ACS Chem. Biol. 15, 618-625 (2020). PMID: 32101404.

Caflisch, A. Kinetic Control of Amyloidogenesis Calls for Unconventional Drugs To Fight Alzheimer's Disease. ACS Chem Neurosci 11, 103-104 (2020). PMID: 31904213.

Cocina, F., Vitalis, A. & Caflisch, A. Sapphire-Based Clustering. J Chem Theory Comput 16, 6383-6396 (2020). PMID: 32905698.

Dolbois, A., Batiste, L., Wiedmer, L., Dong, J., Brütsch, M., Huang, D., Deerain, NM., Spiliotopoulos, D., Cheng-Sánchez, I., Laul, E., Nevado, C., Śledź, P. & Caflisch, A. Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers. ACS Med Chem Lett 11, 1573-1580 (2020). PMID: 32832026.

Goossens, K., Wroblowski, B., Langini, C., Van Vlijmen, H., Caflisch, A. & De Winter, H. Assessment of the fragment docking program SEED. J Chem Inf Model 60, 4881-4893 (2020). PMID: 32820916.

Li, Y., Bedi, RK., Moroz-Omori, EV. & Caflisch, A. Structural and Dynamic Insights into Redundant Function of YTHDF Proteins. J Chem Inf Model 60, 5932-5935 (2020). PMID: 33073985.

Marchand, JR., Knehans, T., Caflisch, A. & Vitalis, A. An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules. J Chem Inf Model 60, 5188-5202 (2020). PMID: 32897071.

Pretze, M., Neuber, C., Kinski, E., Belter, B., Köckerling, M., Caflisch, A., Steinbach, J., Pietzsch, J. & Mamat, C. 18F-labelled xanthine derivatives for PET imaging of Eph receptors. Org. Biomol. Chem. 18, 3104-3116 (2020). PMID: 32253415.

Salutari, I., Martin, R. & Caflisch, A. The 3A6-TCR/superagonist/HLA-DR2a complex shows similar interface and reduced flexibility compared to the complex with self-peptide. Proteins 88, 31-46 (2020). PMID: 31237711.

Unzue, A., Jessen-Trefzer, C., Spiliotopoulos, D., Gaudio, E., Tarantelli, C., Dong, J., Zhao, H., Pachmayr, J., Zahler, S., Bernasconi, E., Sartori, G., Cascione, L., Bertoni, F., Śledź, P., Caflisch, A. & Nevado, C. b]quinoxaline-derivatives as kinase inhibitors. RSC Med Chem 11, 665-675 (2020). PMID: 33479666.

Bacci, M., Caflisch, A. & Vitalis, A. On the removal of initial state bias from simulation data. J Chem Phys 150, 104105 (2019). PMID: 30876362.

Garolini, D., Vitalis, A. & Caflisch, A. Unsupervised identification of states from voltage recordings of neural networks. J. Neurosci. Methods 318, 104-117 (2019). PMID: 30807781.

Gay, JC., Eckenroth, BE., Evans, CM., Langini, C., Carlson, S., Lloyd, JT., Caflisch, A. & Glass, KC. Disulfide bridge formation influences ligand recognition by the ATAD2 bromodomain. Proteins 87, 157-167 (2019). PMID: 30520161.

Ilie, IM. & Caflisch, A. Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chem. Rev. 119, 6956-6993 (2019). PMID: 30973229.

Li, Y., Bedi, RK., Wiedmer, L., Huang, D., Śledź, P. & Caflisch, A. 6A Reader Protein YTHDC1 to Its Preferred RNA Motif. J Chem Theory Comput 15, 7004-7014 (2019). PMID: 31670957.

Wiedmer, L., Schärer, C., Spiliotopoulos, D., Hürzeler, M., Śledź, P. & Caflisch, A. Ligand retargeting by binding site analogy. Eur J Med Chem 175, 107-113 (2019). PMID: 31077996.

Wiedmer, L., Eberle, SA., Bedi, RK., Śledź, P. & Caflisch, A. 6A Writers and Erasers. Anal. Chem. 91, 3078-3084 (2019). PMID: 30715855.

Batiste, L., Unzue, A., Dolbois, A., Hassler, F., Wang, X., Deerain, N., Zhu, J., Spiliotopoulos, D., Nevado, C. & Caflisch, A. Chemical space expansion of bromodomain ligands guided by in silico virtual couplings (AutoCouple). ACS Cent Sci. 4, 180-188 (2018). PMID: 29532017.

Caflisch, A. & Gianni, S. Editorial overview: Folding and binding: In silico, in vitro and in cellula. Curr Opin Struct Biol. 48, iv-vii (2018). PMID: 29475490.

Dalle Vedove, A., Spiliotopoulos, D., D'Agostino, VG., Marchand, JR., Unzue, A., Nevado, C., Lolli, G. & Caflisch, A. Structural analysis of small molecule  binding to the BAZ2A amd BAZ2B bromodomains. ChemMedChem  13, 1479-1487 (2018). PMID: 29770599.

Esposito, C., Wiedmer, L. & Caflisch, A. In silico identification of JMJD3 demethylase inhibitors. J Chem inf Model 58, 2151-2163 (2018). PMID: 30226987.

Esposito, C. & Vitalis, A. Precise estimation of transfer free energies for ionic species between similar media. Phys Chem Chem Phys 20, 27003-27010 (2018). PMID: 30328430.

Ilie, IM. & Caflisch, A. Disorder at the tips of a disease-relevant A beta42 amyloid fibril. A molecular dynamics study. J Phys Chem B. 122, 11072-11082 (2018). PMID: 29965774.

Marchand, JR. & Caflisch, A.In silico fragment-based drug design with SEED. Eur J Med Chem. 156, 907-917 (2018). PMID: 30064119.

Saponara, E., Visentin, M., Baschieri, F., Seleznik, G., Martinelli, P., Esposito, I., Buschmann, J., Chen, R., Parrotta, R., Borgeaud, N., Bombardo, M., Malagola, E., Caflisch, A., Farhan, H., Graf, R.&  Sonda S. Serotonin uptake is required for Rac1 activation in Kras-induced acinar-to-ductal metaplasia in the pancreas. J Pathol. 246, 352-365 (2018). PMID: 30058725.

Śledź, P. & Caflisch, A. Protein structure-based drug design: from docking to molecular dynamics. Curr. Opin. Struct. Biol. 48, 93-102 (2018). PMID: 29149726.

Unzue, A., Cribiú, R., Hoffman, MM., Knehans, T., Lafleur, K., Caflisch, A. & Nevado, C. Iriomoteolides: novel chemical tools to study actin dynamics. Chem Sci. 9, 3793-3802 (2018). PMID: 29780512.

Zhu, J., Zhou, C. & Caflisch, A. Structure-based discovery of selective BRPF1 bromodomain inhibitors. Eur J Med Chem. 155, 337-352 (2018). PMID: 29902720.

Zhu, J., Dong, J., Batiste; L., Unzue, A., Dolbois, A., Pascanu, V., Śledź, P., Nevado, C. &  Caflisch, A. Binding motifs in the CBP bromodomain: an analysis of 20 crystal structures of complexes with small molecules. ACS Med Chem Lett. 9, 929-934 (2018). PMID: 39258543.
Abplanalp, J., Leutert, M., Frugier, E., Nowak, K., Feurer, R., Kato, J., Kistemaker, HVA., Filippov, DV., Moss, J., Caflisch, A. & Hottiger, MO. Proteomic analyses identify ARH3 as a serine mono-ADP-ribosylhydrolase. Nat Commun. 8, 2055 (2017). PMID: 29234005.

Bacci, M., Langini, C., Vymětal, J., Caflisch, A. & Vitalis, A. Focused conformational sampling in proteins. J Chem Phys 147, 195102 (2017). PMID: 29166086. 

Bacci, M., Vymětal, J., Mihajlovic, M., Caflisch. A. & Vitalis, A. Amyloid beta fibril elongation by monomers involves disorder a the tip. J Chem Theory Comput. 13, 5117-5130 (2017). PMID: 28870064.

Ghayor, C., Gjoksi, B., Dong, J., Siegenthaler, B., Caflisch, A. & Weber, FE. N,N Dimethylacetamide a drug excipient that acts as bromodomain ligand for osteoporosis treatment. Sci Rep 7, 42108 (2017).  PMID: 28176838.

Langini, C.,Caflisch, A. & Vitalis, A. The ATAD2 bromodomain binds different acetytation marks on the histone H4 in similar fuzzy complexes. J Biol Chem 292, 16734-16745 (2017). PMID: 28798233 .

Marchand, JR., Vedove, AD., Lollo, G. & Caflisch, A. Discovery of inhibitors of four bromodomains by fragment-anchored ligand docking. J Chem Inf Model. 57, 2584-2597 (2017). PMID: 28862840.

Peón, A., Robles, A., Blanco, B., Convertino, M., Thompson, P., Hawkins, AR., Caflisch, A. & Gonzalez-Bello, C. Reducing the flexibility of type II dehydroquinase enzyme for inhibition - a fragment-base approach and molecular dynamics simulation study.  ChemMedChem. 12, 1512-1524 (2017). PMID: 28791799 

Spiliotopoulos, D., Wamhoff, EC., Lolli, G., Rademacher, C. & Caflisch, A. Discovery of BAZ2A bromodomain ligands. Eur J Med Chem 139, 564-572  (2017). PMID: 28837921.

Spiliotopoulos, D., Zhu, J., Wamhoff, EC., Deerain, N., Marchand, JR., Aretz, J., Rademacher, C. & Caflisch, A. Virtual screen to NMR (VS2NMR): Discovery of fragment hits for the CBP bromodomain. Bioorg. Med. Chem. Lett. 27, 2472-2478 (2017). PMID: 28410781.

Arnon, ZA., Vitalis, A., Levin, A., Michaels, TC., Caflisch, A., Knowles, TP., Adler-Abramovich, L. & Gazit, E. Dynamic microfluidic control of supramolecular peptide self-assembly. Nat Commun 7, 13190 (2016). PMID: 27779182.

Ben Halima, S., Mishra, S., Raja, KM., Willem, M., Baici, A., Simons, K., Brüstle, O., Koch, P., Haass, C., Caflisch, A. & Rajendran, L. Specific Inhibition of β-Secretase Processing of the Alzheimer Disease Amyloid Precursor Protein. Cell Rep 14, 2127-41 (2016). PMID: 26923602.

Lolli, G. & Caflisch, A. High-throughput fragment docking into the BAZ2B bromodomain: Efficient in silico screening for X-ray crystallography. ACS Chem. Biol. 11, 800-7 (2016). PMID: 26942307.

Marchand, JR., Lolli, G. & Caflisch, A. Derivatives of 3-amino-2-methylpyridine as BAZ2B Bromodomain Ligands: in silico Discovery and in crystallo Validation. J. Med. Chem. 59, 9919-9927(2016). PMID: 27731638.

Meyer, PA., Socias, S., Key, J., Ransey, E., Tjon, EC., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D., Rajashankar, K., Anderson, KS., Baxter, RH., Blacklow, SC., Boggon, TJ., Bonvin, AM., Borek, D., Brett, TJ., Caflisch, A., Chang, CI., Chazin, WJ., Corbett, KD., Cosgrove, MS., Crosson, S., Dhe-Paganon, S., Di Cera, E., Drennan, CL., Eck, MJ., Eichman, BF., Fan, QR., Ferré-D'Amaré, AR., Christopher Fromme, J., Garcia, KC., Gaudet, R., Gong, P., Harrison, SC., Heldwein, EE., Jia, Z., Keenan, RJ., Kruse, AC., Kvansakul, M., McLellan, JS., Modis, Y., Nam, Y., Otwinowski, Z., Pai, EF., Pereira, PJ., Petosa, C., Raman, CS., Rapoport, TA., Roll-Mecak, A., Rosen, MK., Rudenko, G., Schlessinger, J., Schwartz, TU., Shamoo, Y., Sondermann, H., Tao, YJ., Tolia, NH., Tsodikov, OV., Westover, KD., Wu, H., Foster, I., Fraser, JS., Maia, FR., Gonen, T., Kirchhausen, T., Diederichs, K., Crosas, M. & Sliz, P. Data publication with the structural biology data grid supports live analysis. Nat Commun 7, 10882 (2016). PMID: 26947396.

Müller, CS., Knehans, T., Davydov, DR., Bounds, PL., von Mandach, U., Halpert, JR., Caflisch, A. & Koppenol, WH. Correction to Concurrent Cooperativity and Substrate Inhibition in the Epoxidation of Carbamazepine by Cytochrome P450 3A4 Active Site Mutants Inspired by Molecular Dynamics Simulations. Biochemistry 55, 5647 (2016). PMID: 27650703.

Reichen, C., Hansen, S., Forzani, C., Honegger, A., Fleishman, SJ., Zhou, T., Parmeggiani, F., Ernst, P., Madhurantakam, C., Ewald, C., Mittl, PR., Zerbe, O., Baker, D., Caflisch, A. & Plückthun, A. Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition. J. Mol. Biol. 428, 4467-4489 (2016). PMID: 27664438.

Roos, M., Pradère, U., Ngondo, RP., Behera, A., Allegrini, S., Civenni, G., Zagalak, JA., Marchand, JR., Menzi, M., Towbin, H., Scheuermann, J., Neri, D., Caflisch, A., Catapano, CV., Ciaudo, C. & Hall, J. A Small-Molecule Inhibitor of Lin28. ACS Chem. Biol. 11, 2773-2781 (2016). PMID: 27548809

Spiliotopoulos, D. & Caflisch, A. Fragment-based in silico screening of bromodomain ligands. Drug Discov Today Technol 19, 81-90 (2016). PMID: 27769362.

Unzue, A., Zhao, H., Lolli, G., Dong, J., Zhu, J., Zechner, M., Dolbois, A., Caflisch, A. & Nevado, C. The "Gatekeeper" Residue Influences the Mode of Binding of Acetyl Indoles to Bromodomains. J. Med. Chem. 59, 3087-97 (2016). PMID: 26982797.

Unzue, A., Lafleur, K., Zhao, H., Zhou, T., Dong, J., Kolb, P., Liebl, J., Zahler, S., Caflisch, A. & Nevado, C. Three stories on Eph kinase inhibitors: From in silico discovery to in vivo validation. Eur J Med Chem  112, 347-66 (2016). PMID: 26907157

Unzue, A., Xu, M., Dong, J., Wiedmer, L., Spiliotopoulos, D., Caflisch, A. & Nevado, C. Fragment-Based Design of Selective Nanomolar Ligands of the CREBBP Bromodomain. J. Med. Chem. 59, 1350-6 (2016). PMID: 26043365.

Xu, M., Caflisch, A. & Hamm, P. Protein structural memory influences ligand binding mode(s) and unbinding rates. J Chem Theory Comput 12, 1393-9 (2016). PMID: 26799675.

Xu, M., Unzue, A., Dong, J., Spiliotopoulos, D., Nevado, C. & Caflisch, A. Discovery of CREBBP Bromodomain Inhibitors by High-Throughput Docking and Hit Optimization Guided by Molecular Dynamics. J. Med. Chem. 59, 1340-9 (2016). PMID: 26125948.

Zhu, J. & Caflisch, A. Twenty Crystal Structures of Bromodomain and PHD Finger Containing Protein 1 (BRPF1)/Ligand Complexes Reveal Conserved Binding Motifs and Rare Interactions. J. Med. Chem. 59, 5555-61 (2016). PMID: 27167503.

Bacci, M., Vitalis, A. & Caflisch, A. A molecular simulation protocol to avoid sampling redundancy and discover new states. Biochim. Biophys. Acta 1850, 889-902 (2015). PMID: 25193737

Blöchliger, N., Caflisch, A. & Vitalis, A. Weighted Distance Functions Improve Analysis of High-Dimensional Data: Application to Molecular Dynamics Simulations. J Chem Theory Comput 11, 5481-92 (2015). PMID: 26574336.

Blöchliger, N., Xu, M. & Caflisch, A. Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges. Biophys. J. 108, 2362-70 (2015). PMID: 25954893.

Dong, J., Zhao, H., Zhou, T., Spiliotopoulos, D., Rajendran, C., Li, XD., Huang, D. & Caflisch, A. Structural Analysis of the Binding of Type I, I1/2, and II Inhibitors to Eph Tyrosine Kinases. ACS Med Chem Lett 6, 79-83 (2015). PMID: 25589935.

Ewald, C., Christen, MT., Watson, RP., Mihajlovic, M., Zhou, T., Honegger, A., Plückthun, A., Caflisch, A. & Zerbe, O. A combined NMR and computational approach to investigate peptide binding to a designed Armadillo repeat protein. J. Mol. Biol. 427, 1916-33 (2015). PMID: 25816772.

Herrmann, US., Schütz, AK., Shirani, H., Huang, D., Saban, D., Nuvolone, M., Li, B., Ballmer, B., Åslund, AK., Mason, JJ., Rushing, E., Budka, H., Nyström, S., Hammarström, P., Böckmann, A., Caflisch, A., Meier, BH., Nilsson, KP., Hornemann, S. & Aguzzi, A. Structure-based drug design identifies polythiophenes as antiprion compounds. Sci Transl Med 7, 299ra123 (2015). PMID: 26246168.

Holehouse, AS., Garai, K., Lyle, N., Vitalis, A. & Pappu, RV. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation. J. Am. Chem. Soc. 137, 2984-95 (2015). PMID: 25664638.

Huang, D. & Caflisch, A. The roles of the conserved tyrosine in the β2-α2 loop of the prion protein. Prion 9, 412-9 (2015). PMID: 26689486.

Huang, D. & Caflisch, A. Evolutionary conserved Tyr169 stabilizes the β2-α2 loop of the prion protein. J. Am. Chem. Soc. 137, 2948-57 (2015). PMID: 25671636.

Marchand, JR. & Caflisch, A. Binding Mode of Acetylated Histones to Bromodomains: Variations on a Common Motif. ChemMedChem 10, 1327-33 (2015). PMID: 26033856.

Müller, CS., Knehans, T., Davydov, DR., Bounds, PL., von Mandach, U., Halpert, JR., Caflisch, A. & Koppenol, WH. Concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations. Biochemistry 54, 711-21 (2015). PMID: 25545162.

Zhao, H. & Caflisch, A. Current kinase inhibitors cover a tiny fraction of fragment space. Bioorg. Med. Chem. Lett. 25, 2372-6 (2015). PMID: 25911301.

Zhao, H. & Caflisch, A. Molecular dynamics in drug design. Eur J Med Chem 91C, 4-14 (2015). PMID: 25108504.

Blöchliger, N., Vitalis, A. & Caflisch, A. High-resolution visualisation of the States and pathways sampled in molecular dynamics simulations. Sci Rep 4, 6264 (2014). PMID: 25179558.

Friedman, R. & Caflisch, A. Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: A simulation study. Proteins 82, 399-404 (2014). PMID: 24038616.

Fu, B., Sahakyan, AB., Camilloni, C., Tartaglia, GG., Paci, E., Caflisch, A., Vendruscolo, M. & Cavalli, A. ALMOST: An all atom molecular simulation toolkit for protein structure determination. J Comput Chem 35, 1101-5 (2014). PMID: 24676684.

Huang, D., Rossini, E., Steiner, S. & Caflisch, A. Structured water molecules in the binding site of bromodomains can be displaced by cosolvent. ChemMedChem 9, 573-9 (2014). PMID: 23804246.

Novinec, M., Korenč, M., Caflisch, A., Ranganathan, R., Lenarčič, B. & Baici, A. A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods. Nat Commun 5, 3287 (2014). PMID: 24518821.

Pevzner, Y., Frugier, E., Schalk, V., Caflisch, A. & Woodcock, HL. Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design. J Chem Inf Model 54, 2612-20 (2014). PMID: 25151852.

Pochorovski, I., Knehans, T., Nettels, D., Müller, AM., Schweizer, WB., Caflisch, A., Schuler, B. & Diederich, F. Experimental and Computational Study of BODIPY Dye-Labeled Cavitand Dynamics. J. Am. Chem. Soc. 136, 2441-9 (2014). PMID: 24490940.

Unzue, A., Dong, J., Lafleur, K., Zhao, H., Frugier, E., Caflisch, A. & Nevado, C. Pyrrolo[3,2-b]quinoxaline Derivatives as Types I1/2 and II Eph Tyrosine Kinase Inhibitors: Structure-Based Design, Synthesis, and in Vivo Validation. J. Med. Chem. 57, 6834-44 (2014). PMID: 25076195.

Vitalis, A. & Caflisch, A. Equilibrium sampling approach to the interpretation of electron density maps. Structure 22, 156-67 (2014). PMID: 24316403.

Watson, RP., Christen, MT., Ewald, C., Bumbak, F., Reichen, C., Mihajlovic, M., Schmidt, E., Güntert, P., Caflisch, A., Plückthun, A. & Zerbe, O. Spontaneous Self-Assembly of Engineered Armadillo Repeat Protein Fragments into a Folded Structure. Structure 22, 985-95 (2014). PMID: 24931467.

Zhao, H., Gartenmann, L., Dong, J., Spiliotopoulos, D. & Caflisch, A. Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking. Bioorg. Med. Chem. Lett. 24, 2493-6 (2014). PMID: 24767840.

Zhao, H. & Caflisch, A. Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk. Bioorg. Med. Chem. Lett. 24, 1523-7 (2014). PMID: 24569110.

Zhou, T., Georgeon, S., Moser, R., Moore, DJ., Caflisch, A. & Hantschel, O. Specificity and mechanism-of-action of the JAK2 tyrosine kinase inhibitors ruxolitinib and SAR302503 (TG101348). Leukemia 28, 471-2 (2014). PMID: 24496285.

Attanasio, F., Convertino, M., Magno, A., Caflisch, A., Corazza, A., Haridas, H., Esposito, G., Cataldo, S., Pignataro, B., Milardi, D. & Rizzarelli, E. Carnosine inhibits ABeta(42) aggregation by perturbing the H-bond network in and around the central hydrophobic cluster. Chembiochem 14, 583-592 (2013).

Buchli, B., Waldauer, SA., Walser, R., Donten, ML., Pfister, R., Blöchliger, N., Steiner, S., Caflisch, A., Zerbe, O. & Hamm, P. Kinetic response of a photoperturbed allosteric protein. PNAS 110, 11725-11730 (2013).

Kalgin, IV., Caflisch, A., Chekmarev,SF. & Karplus, M. New insights into the folding of a beta sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow. J Phys Chem B. 117, 6092-6105 (2013). 

Lafleur, K., Dong, J., Huang, D., Caflisch, A. & Nevado, C. Optimization of inhibitors of the tyrosine kinase EphB4.2. cellular potency improvement and binding mode validation by X-ray crystallography.  J Med Chem. 56, 84-96 (2013).

Rosenthal, F., Feijs, KL., Frugier, E., Bonalli, M., Forst, AH., Imhof, R., Winkler, HC., Fischer, D., Caflisch, A., Hassa, PO., Lüscher, B. & Hottiger, MO. Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases. Nat Struct. Mol. Biol. 20, 502-507 (2013).

Scherzer-Attali, R., Convertino, M., Pellarin, R., Caflisch, A., Gazit, E. & Segal, D. Methylations of tryptophan modified naphtoquinone affect its inhibitory potential towards Abeta aggregation. J Phys Chem B117, 1780-1789 (2013).

Steiner, S, Magno, A., Huang, D. & Caflisch, A. Does bromodomain flexibility influence histone recognition? FEBS Lett. 587, 2158-2163 (2013).

Zhao, H. & Caflisch, A. Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics. Bioorg. Med. Chem. Lett. 23, 5721-6 (2013).

Alfarano, P., Varadamsetty, G., Ewald, C., Parmeggiani, F., Pellarin, R., Zerbe, O., Plückthun, A. & Caflisch, A. Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy. Protein Sci. 21, 1298-1314 ( 2012).

Adler-Abramovich, L., Vaks, L., Carny, O., Trudler, D., Magno, A., Caflisch, A., Frenkel, D. & Gazit, E. Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylkentonuria. Nat Chem Biol 8, 701-706 (2012).

Caflisch, A. & Hamm, P. Complexity in protein folding: simulation meets experiment. Curr Phys Chem. 2, 4-11 (2012).

Huang, D. & Caflisch, A. How does Darunavir prevent HIV-1 protease dimerization? J Chem Theory Comput. 8, 1786-1794 (2012).

Magno, A,, Pellarin, R. & Caflisch, A. Mechanisms and kinetics of amyloid aggregation investigated by a phenomenological coarse-grained model. In: Computational Modelling of Biological Systems, eds. N. Dokholyan, Springer 2012, pp. 191 ff.

Radhakrishnan, A., Vitalis, A., Mao, AH., Steffen, AT. & Pappu, RV. Improved atomistic Monte Carlo simulations demonstrate that poly-l-proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks. J Phys Chem B. 116, 6862-6871 (2012).

Rennebaum, S. & Caflisch, A. Inhibition of interdomain motion in G-actin by the natural product latrunculin: a molecular dynamics study. Proteins. 80, 1998-2008 (2012). 

Scalco, R. & Caflisch, A. Ultrametricity in protein folding dynamics. J Chem Theory Comput. (2012).

Steiner, S. & Caflisch, A. Peptide binding to the PDZ3 domain by conformational selection. Proteins. 80, 2562-2572 (2012).

Vitalis, A. & Caflisch, A. Efficient construction of mesostate networks from molecular dynamics trajectories.  J Chem Theory Comput. 8, 1108-1120 (2012).

Vitalis, A. & Caflisch, A. 50 years of Lifson-Roig models: applications to molecular simulation data. J Chem Theory Comput. 8, 363-373 (2012).

Waldauer,SA., Hassan, S., Paoli, B., Donaldson, PM, Pfister, R., Hamm, P., Caflisch, A. & Pellarin, R. Photocontrol of reversible amyloid formation with a minimal-design peptide. J. Phys. Chem. B. 116, 8961-8973 (2012).

Zhao, H., Huang, D. & Caflisch, A. Discovery of tyrosine kinase inhibitors by docking into an inactive kinase conformation generated by molecular dynamics. ChemMedChem. 2012  Sep 13.  [Epub ahead of print]

Convertino, M., Vitalis, A. & Caflisch, A. Disordered binding of small molecules to A beta12-28. J Biol Chem. 414, 303-312 (2011).

Friedman, R. & Caflisch, A. Surfactant effects of amyloid aggregation kinetics. J Mol. Biol. 414, 303-312 (2011).

Frydman-Marom, A., Convertino. M., Pellarin, R., Lampel, A., Shaltiel-Karyo, R., Segal, D., Caflisch, A., Shalev, DE. & Gazit, E. Structural basis for inhibiting beta amyloid oligomerization by a non-coded beta-breaker-substituted endomorphin analogue. ACS Chem Biol. 6, 1265-1276 (2011).

Ganesan, R., Jelakovic, S., Mittl, PR., Caflisch, A. & Grütter, MG. In silico identification and crystal structure validation of procaspase-3 inhibitors without a P1 aspartic acid moiety. Acta Crystallogr SectF Struct Biol Cryst Commun. 67(Pt8), 842-850 (2011).

Huang, D. & Caflisch, A. Small molecule binding to proteins: affinity and binding/unbinding dynamics from atomistic simulations. Chem Med Chem. 6, 1578-1580 (2011).

Huang, D. & Caflisch, A. The free energy landscape of small molecule unbinding. PLoS Comput. Biol. 7 (2): e1002002 (2011).

Mishra, S. & Caflisch, A .Dynamics in the active site of beta secretase: a network analysis of atomistic simulations. Biochemistry 50, 9328-9339 (2011).

Scalco, R. & Caflisch, A. Equilibrium distribution from distributed computing (simulations of protein folding). J. Phys. Chem B. 115, 6358-6365 (2011).

Seeber, M., Felline, A., Raimondi, F., Muff, S., Friedmann, R., Rao, F., Caflisch, A. & Fanelli, F. Wordom: a user-friendly program for the analysis of molecular structures, trajectories and free energy surfaces. J Comput Chem. 32, 1183-1194 (2011).

Zhao, H. & Huang, D. Hydrogen bond penalty upon ligand binding. PLoS One 6(6): e19923 (2011).

Zheng, W., Qi, B., Rohrdanz, MA., Caflisch, A., Dinner, AR. & Clementi, C. Delineation of folding pathways of a beta-sheet mini-protein. J Phys Chem B. 115, 13065-13074 (2011).

Backus, EH., Bloem, R., Donaldson, PM., Ihalainen, JA., Pfister, R., Paoli, B., Caflisch, A. & Hamm, P. 2D-IR study of a photoswitchable isoptope-labeled alpha-helix. J. Phys. Chem. B. 114, 3735-40 (2010).

Exner,V., Alexandre, C., Rosenfeldt, G., Alfarano, P., Nater, M., Caflisch, A., Gruissem, W., Batschauer, A. & Hennig, L. A gain-of-function mutation of arabidopsis CRYPTOCHROME1 promotes flowering. Plant Physiol. 154, 1633-1645 (2010).

Friedmannn, R. & Caflisch, A. On the orientation of the catalytic dyad in aspartic proteases. Proteins 78, 1575-1582 (2010).  

Friedmannn, R. , Pellarin , R. & Caflisch, A. Soluble protofibrils as metastable intermediates in simulations of amyloid fibril degradation induced by lipid vesicles. J. Physical Chem. Letters 1, 471-474 (2010).

Huang, D., Zhou, T., Lafleur, K., Nevado, C. & Caflisch, A. Kinase selectivity portential for inhibitors targeting the ATP binding site: A network analysis. Bioinformatics 26, 198-204 (2010).

Huang, D. & Caflisch, A. Library screening by fragment-based docking. J. Mol. Recognit. 23, 183-193 (2010).

Kaiser-Bunbury, CN., Muff, S., Memmott, J., Müller, CB. & Caflisch, A. The robustness of pollination networks to the loss of species and interactions: a quantitative approach incorporating pollinator behaviour. Ecol Lett. 13, 442-452  (2010).

Messner S, Altmeyer M, Zhao H, Pozivil A, Roschitzki B, Gehrig P, Rutishauser D, Huang D, Caflisch A &  Hottiger MO. PARP1 ADP-ribosylates lysine residues of the core histone tails. Nucleic Acids Res. 38, 6350-6362 (2010).  

Paoli,B., Pellarin, R. & Caflisch, A. Slow folding of cross-linked alpha-helical peptides due to steric hindrance. J Phys Chem B. 114, 2023-2027 (2010).

Pellarin, R., Schütz, P., Guarnera, E. & Caflisch, A. Amyloid fibril polymorphism is under kinetic control. J Am Chem Soc. 132, 14960-14970 (2010). 

Qi, B., Muff, S., Caflisch, A. & Dinner, AR. Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. J Phys Chem B. 114, 6979-6989 (2010).

Scherzer-Attali, R., Pellarin, R., Convertino, M., Frydman-Marom, A., Egoz-Matia N., Peled, S., Levy-Sakin, M., Shalev, DE., Caflisch, A., Gazit, E. & Segal, D. Complete phenotypic recovery of an Alzheimer's disease model by quinone-tryptophan hybrid aggregation inhibitor. PLoS One. 5(6):e11101 (2010).

Schütz, P., Wuttke, R., Schuler, B. & Caflisch, A. Free energy surfaces from single-distance information. J. Phys. Chem. B. 114, 15227-15235 (2010).  

Sonda S., Morf, L., Bottova, I., Baetschmann, H., Rehrauer, H., Caflisch, A., Hakimi, MA. & Hehl, AB. Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lamblia. Mol Microbiol. 76, 48-67 (2010).

Vitalis, A. & Caflisch, A. Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-beta peptide in aqueous solution and its implications for abeta aggregation. J Mol Biol. 403, 148-165  (2010).

Zhou, T., Lafleur, K. & Caflisch,A. Complementing ultrafast shape recognition with an optical isomerism descriptor. J Mol Graph Model. 29, 443-449 (2010).

Zhou, T. , Huang, D. & Caflisch, A. Quantum mechanical methods for drug design. Curr. Top. Med. Chem 10, 33-45 (2010).

Zhou, T.  & Caflisch, A. High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors. Chem Med Chem. 5, 1007-1014 (2010).

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