Amedeo Caflisch - Publications

Affiliations: 
Universität Zürich, Zürich, ZH, Switzerland 

137 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Li Y, Bedi RK, Wiedmer L, Sun X, Huang D, Caflisch A. Atomistic and Thermodynamic Analysis of N6-Methyladenosine (mA) Recognition by the Reader Domain of YTHDC1. Journal of Chemical Theory and Computation. PMID 33472367 DOI: 10.1021/acs.jctc.0c01136  0.68
2021 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. Chemical Reviews. PMID 33427465 DOI: 10.1021/acs.chemrev.0c00981  0.4
2020 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, et al. Understanding the mechanism of action of pyrrolo[3,2-]quinoxaline-derivatives as kinase inhibitors. Rsc Medicinal Chemistry. 11: 665-675. PMID 33479666 DOI: 10.1039/d0md00049c  0.32
2020 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 Research. PMID 33290556 DOI: 10.1093/nar/gkaa1168  1
2020 Cocina F, Vitalis A, Caflisch A. SAPPHIRE-based clustering. Journal of Chemical Theory and Computation. PMID 32905698 DOI: 10.1021/acs.jctc.0c00604  0.44
2020 Marchand JR, Knehans T, Caflisch A, Vitalis A. An ABSINTH-Based Protocol for Predicting Binding Affinities Between Proteins and Small Molecules. Journal of Chemical Information and Modeling. PMID 32897071 DOI: 10.1021/acs.jcim.0c00558  0.92
2020 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 Medicinal Chemistry Letters. 11: 1573-1580. PMID 32832026 DOI: 10.1021/acsmedchemlett.0c00080  0.68
2020 Bedi RK, Huang D, Eberle SA, Wiedmer L, Caflisch A, Śledź P. Small-molecule inhibitors of METTL3, the major human epitranscriptomic writer. Chemmedchem. PMID 32159918 DOI: 10.1002/cmdc.202000011  0.68
2020 Bedi RK, Huang D, Wiedmer L, Li Y, Dolbois A, Wojdyla JA, Sharpe ME, Caflisch A, Sledz P. Selectively disrupting mA-dependent protein-RNA interactions with fragments. Acs Chemical Biology. PMID 32101404 DOI: 10.1021/acschembio.9b00894  0.68
2019 Li Y, Bedi RK, Wiedmer L, Huang D, Sledz P, Caflisch A. Flexible binding of mA reader protein YTHDC1 to its preferred RNA motif. Journal of Chemical Theory and Computation. PMID 31670957 DOI: 10.1021/acs.jctc.9b00987  0.68
2019 Wiedmer L, Schärer C, Spiliotopoulos D, Hürzeler M, Śledź P, Caflisch A. Ligand retargeting by binding site analogy. European Journal of Medicinal Chemistry. 175: 107-113. PMID 31077996 DOI: 10.1016/j.ejmech.2019.04.037  0.32
2019 Ilie IM, Caflisch A. Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chemical Reviews. PMID 30973229 DOI: 10.1021/acs.chemrev.8b00731  1
2019 Bacci M, Caflisch A, Vitalis A. On the removal of initial state bias from simulation data. The Journal of Chemical Physics. 150: 104105. PMID 30876362 DOI: 10.1063/1.5063556  0.44
2019 Garolini D, Vitalis A, Caflisch A. Unsupervised identification of states from voltage recordings of neural networks. Journal of Neuroscience Methods. PMID 30807781 DOI: 10.1016/j.jneumeth.2019.01.019  0.44
2018 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 Medicinal Chemistry Letters. 9: 929-934. PMID 30258543 DOI: 10.1021/acsmedchemlett.8b00286  0.32
2018 Marchand JR, Caflisch A. In silico fragment-based drug design with SEED. European Journal of Medicinal Chemistry. 156: 907-917. PMID 30064119 DOI: 10.1016/j.ejmech.2018.07.042  0.92
2018 Ilie IM, Caflisch A. Disorder at the Tips of a Disease-Relevant Aβ42 Amyloid Fibril: A Molecular Dynamics Study. The Journal of Physical Chemistry. B. PMID 29965774 DOI: 10.1021/acs.jpcb.8b05236  1
2018 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 and BAZ2B Bromodomains. Chemmedchem. PMID 29770599 DOI: 10.1002/cmdc.201800234  0.92
2018 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 Central Science. 4: 180-188. PMID 29532017 DOI: 10.1021/acscentsci.7b00401  0.32
2017 Langini C, Caflisch A, Vitalis A. The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes. The Journal of Biological Chemistry. 292: 19121. PMID 29373865 DOI: 10.1074/jbc.AAC117.000630  0.44
2017 Bacci M, Langini C, Vymětal J, Caflisch A, Vitalis A. Focused conformational sampling in proteins. The Journal of Chemical Physics. 147: 195102. PMID 29166086 DOI: 10.1063/1.4996879  0.44
2017 Bacci M, Vymětal J, Mihajlovic M, Caflisch A, Vitalis A. Amyloid β Fibril Elongation by Monomers Involves Disorder at the Tip. Journal of Chemical Theory and Computation. PMID 28870064 DOI: 10.1021/acs.jctc.7b00662  0.44
2017 Marchand JR, Vedove AD, Lolli G, Caflisch A. Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. Journal of Chemical Information and Modeling. PMID 28862840 DOI: 10.1021/acs.jcim.7b00336  0.92
2017 Spiliotopoulos D, Wamhoff EC, Lolli G, Rademacher C, Caflisch A. Discovery of BAZ2A bromodomain ligands. European Journal of Medicinal Chemistry. 139: 564-572. PMID 28837921 DOI: 10.1016/j.ejmech.2017.08.028  0.56
2017 Langini C, Caflisch A, Vitalis A. The ATAD2 Bromodomain Binds Different Acetylation Marks on the Histone H4 in Similar Fuzzy Complexes. The Journal of Biological Chemistry. PMID 28798233 DOI: 10.1074/jbc.M117.786350  0.44
2017 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-Based Approach and Molecular Dynamics Simulation Study. Chemmedchem. PMID 28791799 DOI: 10.1002/cmdc.201700396  0.44
2017 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. Bioorganic & Medicinal Chemistry Letters. PMID 28410781 DOI: 10.1016/j.bmcl.2017.04.001  0.92
2016 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. Nature Communications. 7: 13190. PMID 27779182 DOI: 10.1038/ncomms13190  0.44
2016 Spiliotopoulos D, Caflisch A. Fragment-based in silico screening of bromodomain ligands. Drug Discovery Today. Technologies. 19: 81-90. PMID 27769362 DOI: 10.1016/j.ddtec.2016.06.003  0.32
2016 Marchand JR, Lolli G, Caflisch A. Derivatives of 3-amino-2-methylpyridine as BAZ2B Bromodomain Ligands: in silico Discovery and in crystallo Validation. Journal of Medicinal Chemistry. PMID 27731638 DOI: 10.1021/acs.jmedchem.6b01258  0.92
2016 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. Journal of Molecular Biology. PMID 27664438 DOI: 10.1016/j.jmb.2016.09.012  0.4
2016 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. PMID 27650703 DOI: 10.1021/acs.biochem.6b00904  0.4
2016 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, et al. A Small-Molecule Inhibitor of Lin28. Acs Chemical Biology. PMID 27548809 DOI: 10.1021/acschembio.6b00232  0.92
2016 Unzue A, Zhao H, Lolli G, Dong J, Zhu J, Zechner M, Dolbois A, Caflisch A, Nevado C. The "gatekeeper" residue influences the binding mode of acetyl indoles to bromodomains. Journal of Medicinal Chemistry. PMID 26982797 DOI: 10.1021/acs.jmedchem.5b01757  0.92
2016 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, ... ... Caflisch A, et al. Data publication with the structural biology data grid supports live analysis. Nature Communications. 7: 10882. PMID 26947396 DOI: 10.1038/ncomms10882  0.92
2016 Lolli G, Caflisch A. High-Throughput Fragment Docking into the BAZ2B Bromodomain: Efficient in Silico Screening for X-Ray Crystallography. Acs Chemical Biology. 11: 800-7. PMID 26942307 DOI: 10.1021/acschembio.5b00914  0.56
2016 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 Reports. 14: 2127-41. PMID 26923602 DOI: 10.1016/j.celrep.2016.01.076  1
2016 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. European Journal of Medicinal Chemistry. 112: 347-366. PMID 26907157 DOI: 10.1016/j.ejmech.2016.01.057  0.92
2016 Xu M, Caflisch A, Hamm P. Protein structural memory influences ligand binding mode(s) and unbinding rates. Journal of Chemical Theory and Computation. PMID 26799675 DOI: 10.1021/acs.jctc.5b01052  0.92
2016 Lolli G, Caflisch A. High-Throughput Fragment Docking into the BAZ2B Bromodomain: Efficient in Silico Screening for X-Ray Crystallography Acs Chemical Biology. 11: 800-807. DOI: 10.1021/acschembio.5b00914  0.92
2015 Huang D, Caflisch A. The roles of the conserved tyrosine in the β2-α2 loop of the prion protein. Prion. 9: 412-9. PMID 26689486 DOI: 10.1080/19336896.2015.1115944  0.68
2015 Blöchliger N, Caflisch A, Vitalis A. Weighted Distance Functions Improve Analysis of High-Dimensional Data: Application to Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 11: 5481-92. PMID 26574336 DOI: 10.1021/acs.jctc.5b00618  0.92
2015 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, et al. Structure-based drug design identifies polythiophenes as antiprion compounds. Science Translational Medicine. 7: 299ra123. PMID 26246168 DOI: 10.1126/scitranslmed.aab1923  0.92
2015 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. Journal of Medicinal Chemistry. PMID 26125948 DOI: 10.1021/acs.jmedchem.5b00171  0.92
2015 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. Journal of Medicinal Chemistry. PMID 26043365 DOI: 10.1021/acs.jmedchem.5b00172  0.92
2015 Marchand JR, Caflisch A. Binding Mode of Acetylated Histones to Bromodomains: Variations on a Common Motif. Chemmedchem. 10: 1327-33. PMID 26033856 DOI: 10.1002/cmdc.201500141  0.92
2015 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. Journal of Molecular Biology. 427: 1916-33. PMID 25816772 DOI: 10.1016/j.jmb.2015.02.022  0.92
2015 Huang D, Caflisch A. Evolutionary conserved Tyr169 stabilizes the β2-α2 loop of the prion protein. Journal of the American Chemical Society. 137: 2948-57. PMID 25671636 DOI: 10.1021/ja511568m  0.68
2015 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 Medicinal Chemistry Letters. 6: 79-83. PMID 25589935 DOI: 10.1021/ml500355x  0.68
2015 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. PMID 25545162 DOI: 10.1021/bi5011656  0.92
2015 Bacci M, Vitalis A, Caflisch A. A molecular simulation protocol to avoid sampling redundancy and discover new states. Biochimica Et Biophysica Acta. 1850: 889-902. PMID 25193737 DOI: 10.1016/j.bbagen.2014.08.013  0.92
2014 Blöchliger N, Vitalis A, Caflisch A. High-resolution visualisation of the states and pathways sampled in molecular dynamics simulations. Scientific Reports. 4: 6264. PMID 25179558 DOI: 10.1038/srep06264  0.92
2014 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 Journal of Medicinal Chemistry. 57: 6834-6844. PMID 25076195 DOI: 10.1021/jm5009242  0.92
2014 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 (London, England : 1993). 22: 985-95. PMID 24931467 DOI: 10.1016/j.str.2014.05.002  0.92
2014 Zhao H, Gartenmann L, Dong J, Spiliotopoulos D, Caflisch A. Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking. Bioorganic & Medicinal Chemistry Letters. 24: 2493-6. PMID 24767840 DOI: 10.1016/j.bmcl.2014.04.017  0.32
2014 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. Journal of Computational Chemistry. 35: 1101-5. PMID 24676684 DOI: 10.1002/jcc.23588  0.92
2014 Novinec M, Koren? M, Caflisch A, Ranganathan R, Lenar?i? B, Baici A. A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods. Nature Communications. 5: 3287. PMID 24518821 DOI: 10.1038/ncomms4287  0.92
2014 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. Journal of the American Chemical Society. 136: 2441-9. PMID 24490940 DOI: 10.1021/ja4104292  0.4
2014 Vitalis A, Caflisch A. Equilibrium sampling approach to the interpretation of electron density maps. Structure (London, England : 1993). 22: 156-67. PMID 24316403 DOI: 10.1016/j.str.2013.10.014  0.92
2014 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. PMID 23804246 DOI: 10.1002/cmdc.201300156  0.68
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. Proceedings of the National Academy of Sciences of the United States of America. 110: 11725-30. PMID 23818626 DOI: 10.1073/pnas.1306323110  0.92
2013 Steiner S, Magno A, Huang D, Caflisch A. Does bromodomain flexibility influence histone recognition? Febs Letters. 587: 2158-63. PMID 23711371 DOI: 10.1016/j.febslet.2013.05.032  0.68
2013 Kalgin IV, Caflisch A, Chekmarev SF, Karplus M. New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow. The Journal of Physical Chemistry. B. 117: 6092-105. PMID 23621790 DOI: 10.1021/jp401742y  0.92
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. Nature Structural & Molecular Biology. 20: 502-7. PMID 23474714 DOI: 10.1038/nsmb.2521  0.92
2013 Attanasio F, Convertino M, Magno A, Caflisch A, Corazza A, Haridas H, Esposito G, Cataldo S, Pignataro B, Milardi D, Rizzarelli E. Carnosine inhibits Aβ(42) aggregation by perturbing the H-bond network in and around the central hydrophobic cluster. Chembiochem : a European Journal of Chemical Biology. 14: 583-92. PMID 23440928 DOI: 10.1002/cbic.201200704  0.44
2013 Scherzer-Attali R, Convertino M, Pellarin R, Gazit E, Segal D, Caflisch A. Methylations of tryptophan-modified naphthoquinone affect its inhibitory potential toward Aβ aggregation. The Journal of Physical Chemistry. B. 117: 1780-9. PMID 23259849 DOI: 10.1021/jp309066p  0.92
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 Journal of Medicinal Chemistry. 56: 84-96. PMID 23253074 DOI: 10.1021/jm301187e  0.92
2013 Blöchliger N, Vitalis A, Caflisch A. A scalable algorithm to order and annotate continuous observations reveals the metastable states visited by dynamical systems Computer Physics Communications. 184: 2446-2453. DOI: 10.1016/j.cpc.2013.06.009  0.92
2012 Huang D, Caflisch A. How Does Darunavir Prevent HIV-1 Protease Dimerization? Journal of Chemical Theory and Computation. 8: 1786-94. PMID 26593669 DOI: 10.1021/ct300032r  0.68
2012 Vitalis A, Caflisch A. Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories. Journal of Chemical Theory and Computation. 8: 1108-20. PMID 26593370 DOI: 10.1021/ct200801b  0.92
2012 Vitalis A, Caflisch A. 50 Years of Lifson-Roig Models: Application to Molecular Simulation Data. Journal of Chemical Theory and Computation. 8: 363-73. PMID 26592894 DOI: 10.1021/ct200744s  0.92
2012 Zhao H, Dong J, Lafleur K, Nevado C, Caflisch A. Discovery of a novel chemotype of tyrosine kinase inhibitors by fragment-based docking and molecular dynamics. Acs Medicinal Chemistry Letters. 3: 834-8. PMID 24900387 DOI: 10.1021/ml3001984  0.32
2012 Zhao H, Huang D, Caflisch A. Discovery of tyrosine kinase inhibitors by docking into an inactive kinase conformation generated by molecular dynamics. Chemmedchem. 7: 1983-90. PMID 22976951 DOI: 10.1002/cmdc.201200331  0.68
2012 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 Science : a Publication of the Protein Society. 21: 1298-314. PMID 22767482 DOI: 10.1002/pro.2117  0.92
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. The Journal of Physical Chemistry. B. 116: 8961-73. PMID 22724381 DOI: 10.1021/jp305311z  0.92
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 phenylketonuria. Nature Chemical Biology. 8: 701-6. PMID 22706200 DOI: 10.1038/nchembio.1002  0.92
2012 Zhao H, Dong J, Lafleur K, Nevado C, Caflisch A. Discovery of a novel chemotype of tyrosine kinase inhibitors by fragment-based docking and molecular dynamics Acs Medicinal Chemistry Letters. 3: 834-838. DOI: 10.1021/ml3001984  0.92
2011 Convertino M, Vitalis A, Caflisch A. Disordered binding of small molecules to Aβ(12-28). The Journal of Biological Chemistry. 286: 41578-88. PMID 21969380 DOI: 10.1074/jbc.M111.285957  0.92
2011 Zheng W, Qi B, Rohrdanz MA, Caflisch A, Dinner AR, Clementi C. Delineation of folding pathways of a β-sheet miniprotein. The Journal of Physical Chemistry. B. 115: 13065-74. PMID 21942785 DOI: 10.1021/jp2076935  0.92
2011 Mishra S, Caflisch A. Dynamics in the active site of β-secretase: a network analysis of atomistic simulations. Biochemistry. 50: 9328-39. PMID 21942621 DOI: 10.1021/bi2011948  1
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 β-amyloid oligomerization by a non-coded β-breaker-substituted endomorphin analogue. Acs Chemical Biology. 6: 1265-76. PMID 21892833 DOI: 10.1021/cb200103h  0.92
2011 Huang D, Caflisch A. Small molecule binding to proteins: affinity and binding/unbinding dynamics from atomistic simulations. Chemmedchem. 6: 1578-80. PMID 21674810 DOI: 10.1002/cmdc.201100237  0.68
2011 Huang D, Caflisch A. The free energy landscape of small molecule unbinding. Plos Computational Biology. 7: e1002002. PMID 21390201 DOI: 10.1371/journal.pcbi.1002002  0.68
2011 Seeber M, Felline A, Raimondi F, Muff S, Friedman R, Rao F, Caflisch A, Fanelli F. Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. Journal of Computational Chemistry. 32: 1183-94. PMID 21387345 DOI: 10.1002/jcc.21688  0.92
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 Physiology. 154: 1633-45. PMID 20926618 DOI: 10.1104/pp.110.160895  0.92
2010 Pellarin R, Schuetz P, Guarnera E, Caflisch A. Amyloid fibril polymorphism is under kinetic control. Journal of the American Chemical Society. 132: 14960-70. PMID 20923147 DOI: 10.1021/ja106044u  0.4
2010 Vitalis A, Caflisch A. Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-β peptide in aqueous solution and its implications for Aβ aggregation. Journal of Molecular Biology. 403: 148-65. PMID 20709081 DOI: 10.1016/j.jmb.2010.08.003  0.92
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 a quinone-tryptophan hybrid aggregation inhibitor. Plos One. 5: e11101. PMID 20559435 DOI: 10.1371/journal.pone.0011101  0.92
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 Research. 38: 6350-62. PMID 20525793 DOI: 10.1093/nar/gkq463  0.92
2010 Qi B, Muff S, Caflisch A, Dinner AR. Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. The Journal of Physical Chemistry. B. 114: 6979-89. PMID 20438066 DOI: 10.1021/jp101476g  0.92
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. Ecology Letters. 13: 442-52. PMID 20100244 DOI: 10.1111/j.1461-0248.2009.01437.x  0.68
2010 Huang D, Zhou T, Lafleur K, Nevado C, Caflisch A. Kinase selectivity potential for inhibitors targeting the ATP binding site: A network analysis Bioinformatics. 26: 198-204. PMID 19942586 DOI: 10.1093/bioinformatics/btp650  0.92
2010 Zhou T, Huang D, Caflisch A. Quantum mechanical methods for drug design. Current Topics in Medicinal Chemistry. 10: 33-45. PMID 19929831  0.68
2010 Huang D, Caflisch A. Library screening by fragment-based docking. Journal of Molecular Recognition : Jmr. 23: 183-93. PMID 19718684 DOI: 10.1002/jmr.981  0.68
2009 Lafleur K, Huang D, Zhou T, Caflisch A, Nevado C. Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4) Journal of Medicinal Chemistry. 52: 6433-6446. PMID 19788238 DOI: 10.1021/jm9009444  0.92
2009 Guarnera E, Pellarin R, Caflisch A. How does a simplified-sequence protein fold? Biophysical Journal. 97: 1737-46. PMID 19751679 DOI: 10.1016/j.bpj.2009.06.047  0.4
2009 Bodenreider C, Beer D, Keller TH, Sonntag S, Wen D, Yap L, Yau YH, Shochat SG, Huang D, Zhou T, Caflisch A, Su XC, Ozawa K, Otting G, Vasudevan SG, et al. A fluorescence quenching assay to discriminate between specific and nonspecific inhibitors of dengue virus protease. Analytical Biochemistry. 395: 195-204. PMID 19682971 DOI: 10.1016/j.ab.2009.08.013  0.68
2009 Su XC, Ozawa K, Yagi H, Lim SP, Wen D, Ekonomiuk D, Huang D, Keller TH, Sonntag S, Caflisch A, Vasudevan SG, Otting G. NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease. The Febs Journal. 276: 4244-55. PMID 19583774 DOI: 10.1111/j.1742-4658.2009.07132.x  0.68
2009 Ekonomiuk D, Su XC, Ozawa K, Bodenreider C, Lim SP, Otting G, Huang D, Caflisch A. Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics. Journal of Medicinal Chemistry. 52: 4860-8. PMID 19572550 DOI: 10.1021/jm900448m  0.68
2009 Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, et al. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry. 30: 1545-614. PMID 19444816 DOI: 10.1002/jcc.21287  0.92
2009 Exner V, Aichinger E, Shu H, Wildhaber T, Alfarano P, Caflisch A, Gruissem W, Köhler C, Hennig L. The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development. Plos One. 4: e5335. PMID 19399177 DOI: 10.1371/journal.pone.0005335  0.92
2009 Convertino M, Pellarin R, Catto M, Carotti A, Caflisch A. 9,10-Anthraquinone hinders beta-aggregation: how does a small molecule interfere with Abeta-peptide amyloid fibrillation? Protein Science : a Publication of the Protein Society. 18: 792-800. PMID 19309732 DOI: 10.1002/pro.87  0.44
2009 Paoli B, Seeber M, Backus EH, Ihalainen JA, Hamm P, Caflisch A. Bulky side chains and non-native salt bridges slow down the folding of a cross-linked helical peptide: a combined molecular dynamics and time-resolved infrared spectroscopy study. The Journal of Physical Chemistry. B. 113: 4435-42. PMID 19256526 DOI: 10.1021/jp810431s  0.92
2009 Ekonomiuk D, Su XC, Ozawa K, Bodenreider C, Lim SP, Yin Z, Keller TH, Beer D, Patel V, Otting G, Caflisch A, Huang D. Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking. Plos Neglected Tropical Diseases. 3: e356. PMID 19159012 DOI: 10.1371/journal.pntd.0000356  0.68
2009 Friedman R, Pellarin R, Caflisch A. Amyloid aggregation on lipid bilayers and its impact on membrane permeability. Journal of Molecular Biology. 387: 407-15. PMID 19133272 DOI: 10.1016/j.jmb.2008.12.036  0.4
2008 Schenker P, Alfarano P, Kolb P, Caflisch A, Baici A. A double-headed cathepsin B inhibitor devoid of warhead. Protein Science : a Publication of the Protein Society. 17: 2145-55. PMID 18796695 DOI: 10.1110/ps.037341.108  0.92
2008 Ihalainen JA, Paoli B, Muff S, Backus EH, Bredenbeck J, Woolley GA, Caflisch A, Hamm P. Alpha-Helix folding in the presence of structural constraints. Proceedings of the National Academy of Sciences of the United States of America. 105: 9588-93. PMID 18621686 DOI: 10.1073/pnas.0712099105  0.68
2008 Krivov SV, Muff S, Caflisch A, Karplus M. One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process. The Journal of Physical Chemistry. B. 112: 8701-14. PMID 18590307 DOI: 10.1021/jp711864r  0.92
2008 Zhou T, Huang D, Caflisch A. Is quantum mechanics necessary for predicting binding free energy? Journal of Medicinal Chemistry. 51: 4280-8. PMID 18578469 DOI: 10.1021/jm800242q  0.68
2008 Kolb P, Kipouros CB, Huang D, Caflisch A. Structure-based tailoring of compound libraries for high-throughput screening: discovery of novel EphB4 kinase inhibitors. Proteins. 73: 11-8. PMID 18384152 DOI: 10.1002/prot.22028  0.92
2008 Dey F, Caflisch A. Fragment-based de novo ligand design by multiobjective evolutionary optimization. Journal of Chemical Information and Modeling. 48: 679-90. PMID 18307332 DOI: 10.1021/ci700424b  0.44
2008 Kolb P, Huang D, Dey F, Caflisch A. Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model. Journal of Medicinal Chemistry. 51: 1179-88. PMID 18271520 DOI: 10.1021/jm070654j  0.92
2008 Parmeggiani F, Pellarin R, Larsen AP, Varadamsetty G, Stumpp MT, Zerbe O, Caflisch A, Plückthun A. Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core. Journal of Molecular Biology. 376: 1282-304. PMID 18222472 DOI: 10.1016/j.jmb.2007.12.014  0.92
2008 Interlandi G, Wetzel SK, Settanni G, Plückthun A, Caflisch A. Characterization and further stabilization of designed ankyrin repeat proteins by combining molecular dynamics simulations and experiments. Journal of Molecular Biology. 375: 837-54. PMID 18048057 DOI: 10.1016/j.jmb.2007.09.042  0.92
2007 Seeber M, Cecchini M, Rao F, Settanni G, Caflisch A. Wordom: A program for efficient analysis of molecular dynamics simulations Bioinformatics. 23: 2625-2627. PMID 17717034 DOI: 10.1093/bioinformatics/btm378  0.92
2006 Kolb P, Caflisch A. Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking. Journal of Medicinal Chemistry. 49: 7384-92. PMID 17149868 DOI: 10.1021/jm060838i  0.92
2006 Seeber M, Fanelli F, Paci E, Caflisch A. Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane Biophysical Journal. 91: 3276-3284. PMID 16861280 DOI: 10.1529/biophysj.106.088591  0.92
2006 Huang D, Lüthi U, Kolb P, Cecchini M, Barberis A, Caflisch A. In silico discovery of beta-secretase inhibitors. Journal of the American Chemical Society. 128: 5436-43. PMID 16620115 DOI: 10.1021/ja0573108  0.92
2006 Cecchini M, Curcio R, Pappalardo M, Melki R, Caflisch A. A molecular dynamics approach to the structural characterization of amyloid aggregation. Journal of Molecular Biology. 357: 1306-21. PMID 16483608 DOI: 10.1016/j.jmb.2006.01.009  0.56
2005 Curcio R, Caflisch A, Paci E. Change of the unbinding mechanism upon a mutation: a molecular dynamics study of an antibody-hapten complex. Protein Science : a Publication of the Protein Society. 14: 2499-514. PMID 16195542 DOI: 10.1110/ps.041280705  0.4
2005 Huang D, Lüthi U, Kolb P, Edler K, Cecchini M, Audetat S, Barberis A, Caflisch A. Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations. Journal of Medicinal Chemistry. 48: 5108-11. PMID 16078830 DOI: 10.1021/jm050499d  0.92
2004 Cecchini M, Rao F, Seeber M, Caflisch A. Replica exchange molecular dynamics simulations of amyloid peptide aggregation Journal of Chemical Physics. 121: 10748-10756. PMID 15549960 DOI: 10.1063/1.1809588  0.92
2004 Levy Y, Caflisch A, Onuchic JN, Wolynes PG. The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations. Journal of Molecular Biology. 340: 67-79. PMID 15184023 DOI: 10.1016/j.jmb.2004.04.028  0.92
2004 Cecchini M, Kolb P, Majeux N, Caflisch A. Automated docking of highly flexible ligands by genetic algorithms: a critical assessment. Journal of Computational Chemistry. 25: 412-22. PMID 14696075 DOI: 10.1002/jcc.10384  0.92
2003 Paci E, Cavalli A, Vendruscolo M, Caflisch A. Analysis of the distributed computing approach applied to the folding of a small beta peptide. Proceedings of the National Academy of Sciences of the United States of America. 100: 8217-22. PMID 12815104 DOI: 10.1073/pnas.1331838100  0.4
2003 Uk B, Taufer M, Stricker T, Settanni G, Cavalli A, Caflisch A. Combining task- and data parallelism to speed up protein folding on a desktop grid platform Proceedings - Ccgrid 2003: 3rd Ieee/Acm International Symposium On Cluster Computing and the Grid. 240-249. DOI: 10.1109/CCGRID.2003.1199374  0.92
2003 Levy Y, Caflisch A. Flexibility of monomeric and dimeric HIV-1 protease Journal of Physical Chemistry B. 107: 3068-3079. DOI: 10.1021/jp0219956  0.92
2002 Taufer M, Perathoner E, Cavalli A, Caflisch A, Stricker T. Performance characterization of a molecular dynamics code on PC clusters: Is there any easy parallelism in CHARMM? Proceedings - International Parallel and Distributed Processing Symposium, Ipdps 2002. 282-289. DOI: 10.1109/IPDPS.2002.1015505  0.92
2001 Paci E, Caflisch A, Plückthun A, Karplus M. Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study Journal of Molecular Biology. 314: 589-605. PMID 11846569 DOI: 10.1006/jmbi.2001.5103  0.92
2000 Caflisch A, Schramm HJ, Karplus M. Design of dimerization inhibitors of HIV-1 aspartic proteinase: a computer-based combinatorial approach. Journal of Computer-Aided Molecular Design. 14: 161-79. PMID 10721504 DOI: 10.1023/A:1008146201260  1
1999 Caflisch A, Karplus M. Structural details of urea binding to barnase: a molecular dynamics analysis. Structure (London, England : 1993). 7: 477-88. PMID 10378267 DOI: 10.1016/S0969-2126(99)80064-1  1
1997 Caflisch A, Fischer S, Karplus M. Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP?substrate complex Journal of Computational Chemistry. 18: 723-743. DOI: 10.1002/(SICI)1096-987X(19970430)18:6<723::AID-JCC1>3.0.CO;2-U  1
1995 Caflisch A, Karplus M. Acid and thermal denaturation of barnase investigated by molecular dynamics simulations. Journal of Molecular Biology. 252: 672-708. PMID 7563082 DOI: 10.1006/jmbi.1995.0528  1
1995 Caflisch A, Karplus M. Computational combinatorial chemistry for de novo ligand design: Review and assessment Perspectives in Drug Discovery and Design. 3: 51-84. DOI: 10.1007/BF02174467  1
1995 Karplus M, Caflisch A, Săli A, Shakhnovich E. Protein dynamics: From the native to the unfolded state and back again Molecular Engineering. 5: 55-70. DOI: 10.1007/BF00999578  1
1994 Caflisch A, Karplus M. Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase. Proceedings of the National Academy of Sciences of the United States of America. 91: 1746-50. PMID 8127876 DOI: 10.1073/pnas.91.5.1746  1
1993 Caflisch A, Miranker A, Karplus M. Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase. Journal of Medicinal Chemistry. 36: 2142-67. PMID 8340918 DOI: 10.1021/jm00067a013  1
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