| Year |
Citation |
Score |
| 2024 |
Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, et al. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. The Journal of Physical Chemistry. B. PMID 39303207 DOI: 10.1021/acs.jpcb.4c04100 |
0.697 |
|
| 2024 |
Zhou J, Assenza S, Tatli M, Tian J, Ilie IM, Starostin EL, Caflisch A, Knowles TPJ, Dietler G, Ruggeri FS, Stahlberg H, Sekatskii SK, Mezzenga R. Hierarchical Protofilament Intertwining Rules the Formation of Mixed-Curvature Amyloid Polymorphs. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). e2402740. PMID 38899849 DOI: 10.1002/advs.202402740 |
0.677 |
|
| 2024 |
Corbeski I, Vargas-Rosales PA, Bedi RK, Deng J, Coelho D, Braud E, Iannazzo L, Li Y, Huang D, Ethève-Quelquejeu M, Cui Q, Caflisch A. The catalytic mechanism of the RNA methyltransferase METTL3. Elife. 12. PMID 38470714 DOI: 10.7554/eLife.92537 |
0.448 |
|
| 2023 |
Corbeski I, Vargas-Rosales PA, Bedi RK, Deng J, Coelho D, Braud E, Iannazzo L, Li Y, Huang D, Ethève-Quelquejeu M, Cui Q, Caflisch A. The catalytic mechanism of the RNA methyltransferase METTL3. Biorxiv : the Preprint Server For Biology. PMID 37732228 DOI: 10.1101/2023.09.06.556513 |
0.449 |
|
| 2023 |
Ilie IM, Ehrhardt C, Caflisch A, Weitz-Schmidt G. Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. 63: 3878-3891. PMID 37310029 DOI: 10.1021/acs.jcim.3c00480 |
0.698 |
|
| 2022 |
Dehabadi MH, Caflisch A, Ilie IM, Firouzi R. Interactions of Curcumin's Degradation Products with the Aβ Dimer: A Computational Study. The Journal of Physical Chemistry. B. PMID 36148988 DOI: 10.1021/acs.jpcb.2c05846 |
0.73 |
|
| 2022 |
Nai F, Nachawati R, Zálešák F, Wang X, Li Y, Caflisch A. Fragment Ligands of the mA-RNA Reader YTHDF2. Acs Medicinal Chemistry Letters. 13: 1500-1509. PMID 36110386 DOI: 10.1021/acsmedchemlett.2c00303 |
0.345 |
|
| 2022 |
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 Medicinal Chemistry Letters. 13: 1434-1443. PMID 36105334 DOI: 10.1021/acsmedchemlett.2c00173 |
0.795 |
|
| 2022 |
Ilie IM, Caflisch A. Antibody binding increases the flexibility of the prion protein. Biochimica Et Biophysica Acta. Proteins and Proteomics. 140827. PMID 35931365 DOI: 10.1016/j.bbapap.2022.140827 |
0.705 |
|
| 2022 |
Ilie IM, Bacci M, Vitalis A, Caflisch A. Antibody binding modulates the dynamics of the membrane-bound prion protein. Biophysical Journal. PMID 35672948 DOI: 10.1016/j.bpj.2022.06.007 |
0.699 |
|
| 2022 |
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. Biochimica Et Biophysica Acta. Proteins and Proteomics. 1870: 140772. PMID 35307557 DOI: 10.1016/j.bbapap.2022.140772 |
0.716 |
|
| 2021 |
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. Biochimica Et Biophysica Acta. Biomembranes. 183825. PMID 34871574 DOI: 10.1016/j.bbamem.2021.183825 |
0.693 |
|
| 2021 |
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. The Journal of Biological Chemistry. 101403. PMID 34793836 DOI: 10.1016/j.jbc.2021.101403 |
0.688 |
|
| 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 |
0.32 |
|
| 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 |
0.666 |
|
| 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 |
0.803 |
|
| 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 |
0.434 |
|
| 2020 |
Goossens K, Wroblowski B, Langini C, van Vlijmen H, Caflisch A, De Winter H. Assessment of the Fragment Docking Program SEED. Journal of Chemical Information and Modeling. PMID 32820916 DOI: 10.1021/Acs.Jcim.0C00556 |
0.645 |
|
| 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 |
0.372 |
|
| 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: 10.2210/Pdb6Szr/Pdb |
0.412 |
|
| 2020 |
Caflisch A. Kinetic Control of Amyloidogenesis Calls for Unconventional Drugs To Fight Alzheimer's Disease. Acs Chemical Neuroscience. 11: 103-104. PMID 31904213 DOI: 10.1021/Acschemneuro.9B00676 |
0.333 |
|
| 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: 10.2210/Pdb6Rt5/Pdb |
0.37 |
|
| 2019 |
Salutari I, Martin R, Caflisch A. A TCR/superagonist/MHC complex shows similar interface and reduced flexibility compared to the complex with self-peptide. Proteins. PMID 31237711 DOI: 10.1002/Prot.25764 |
0.326 |
|
| 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 |
0.437 |
|
| 2019 |
Ilie IM, Caflisch A. Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chemical Reviews. PMID 30973229 DOI: 10.1021/Acs.Chemrev.8B00731 |
0.728 |
|
| 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 |
0.312 |
|
| 2019 |
Wiedmer L, Eberle SA, Bedi RK, Śledź P, Caflisch A. A Reader-Based Assay for mA Writers and Erasers. Analytical Chemistry. PMID 30715855 DOI: 10.1021/Acs.Analchem.8B05500 |
0.337 |
|
| 2019 |
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. PMID 30520161 DOI: 10.1002/Prot.25636 |
0.438 |
|
| 2019 |
Caflisch A, Wälchli R, Ehrhardt C. Computer-Aided Design of Thrombin Inhibitors. News in Physiological Sciences : An International Journal of Physiology Produced Jointly by the International Union of Physiological Sciences and the American Physiological Society. 13: 182-189. PMID 11390786 DOI: 10.1152/Physiologyonline.1998.13.4.182 |
0.31 |
|
| 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: 10.2210/Pdb6Fqu/Pdb |
0.396 |
|
| 2018 |
Esposito C, Wiedmer L, Caflisch A. In Silico Identification of JMJD3 Demethylase Inhibitors. Journal of Chemical Information and Modeling. PMID 30226987 DOI: 10.1021/Acs.Jcim.8B00539 |
0.399 |
|
| 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 |
0.791 |
|
| 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 |
0.732 |
|
| 2018 |
Zhu J, Zhou C, Caflisch A. Structure-based discovery of selective BRPF1 bromodomain inhibitors. European Journal of Medicinal Chemistry. 155: 337-352. PMID 29902720 DOI: 10.1016/J.Ejmech.2018.05.037 |
0.413 |
|
| 2018 |
Unzue A, Cribiú R, Hoffman MM, Knehans T, Lafleur K, Caflisch A, Nevado C. Iriomoteolides: novel chemical tools to study actin dynamics. Chemical Science. 9: 3793-3802. PMID 29780512 DOI: 10.1039/C7Sc04286H |
0.308 |
|
| 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 |
0.804 |
|
| 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 |
0.363 |
|
| 2018 |
Caflisch A, Gianni S. Editorial overview: Folding and binding: In silico, in vitro and in cellula. Current Opinion in Structural Biology. 48: iv-vii. PMID 29475490 DOI: 10.1016/J.Sbi.2018.01.014 |
0.337 |
|
| 2017 |
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. Nature Communications. 8: 2055. PMID 29234005 DOI: 10.1038/S41467-017-02253-1 |
0.333 |
|
| 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 |
0.354 |
|
| 2017 |
Śledź P, Caflisch A. Protein structure-based drug design: from docking to molecular dynamics. Current Opinion in Structural Biology. 48: 93-102. PMID 29149726 DOI: 10.1016/J.Sbi.2017.10.010 |
0.435 |
|
| 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 |
0.382 |
|
| 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 |
0.802 |
|
| 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 |
0.411 |
|
| 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 |
0.386 |
|
| 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 |
0.733 |
|
| 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 |
0.796 |
|
| 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 |
0.301 |
|
| 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 |
0.401 |
|
| 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 |
0.79 |
|
| 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 |
0.417 |
|
| 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 |
0.784 |
|
| 2016 |
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. Journal of Medicinal Chemistry. PMID 27167503 DOI: 10.1021/Acs.Jmedchem.6B00215 |
0.396 |
|
| 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 |
0.391 |
|
| 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 |
0.393 |
|
| 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 |
0.638 |
|
| 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 |
0.597 |
|
| 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 |
0.392 |
|
| 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 |
0.373 |
|
| 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 |
0.326 |
|
| 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 |
0.392 |
|
| 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 |
0.416 |
|
| 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 |
0.389 |
|
| 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 |
0.789 |
|
| 2015 |
Blöchliger N, Xu M, Caflisch A. Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges. Biophysical Journal. 108: 2362-70. PMID 25954893 DOI: 10.1016/J.Bpj.2015.03.038 |
0.411 |
|
| 2015 |
Zhao H, Caflisch A. Current kinase inhibitors cover a tiny fraction of fragment space. Bioorganic & Medicinal Chemistry Letters. 25: 2372-6. PMID 25911301 DOI: 10.1016/J.Bmcl.2015.04.005 |
0.334 |
|
| 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 |
0.435 |
|
| 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 |
0.312 |
|
| 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 |
0.336 |
|
| 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 |
0.366 |
|
| 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 |
0.305 |
|
| 2015 |
Zhao H, Caflisch A. Molecular dynamics in drug design. European Journal of Medicinal Chemistry. 91: 4-14. PMID 25108504 DOI: 10.1016/J.Ejmech.2014.08.004 |
0.42 |
|
| 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 |
0.332 |
|
| 2014 |
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. Journal of Chemical Information and Modeling. 54: 2612-20. PMID 25151852 DOI: 10.1021/Ci500322K |
0.317 |
|
| 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 |
0.314 |
|
| 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 |
0.364 |
|
| 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 |
0.397 |
|
| 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 |
0.534 |
|
| 2014 |
Zhao H, Caflisch A. Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk. Bioorganic & Medicinal Chemistry Letters. 24: 1523-7. PMID 24569110 DOI: 10.1016/J.Bmcl.2014.01.083 |
0.315 |
|
| 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 |
0.362 |
|
| 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 |
0.339 |
|
| 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 |
0.309 |
|
| 2014 |
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. PMID 24038616 DOI: 10.1002/Prot.24402 |
0.37 |
|
| 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 |
0.383 |
|
| 2014 |
Spiliotopoulos D, Caflisch A. Molecular Dynamics Simulations of Bromodomains Reveal Binding-Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl-Lysine Israel Journal of Chemistry. 54: 1084-1092. DOI: 10.1002/Ijch.201400009 |
0.416 |
|
| 2013 |
Magno A, Steiner S, Caflisch A. Mechanism and Kinetics of Acetyl-Lysine Binding to Bromodomains. Journal of Chemical Theory and Computation. 9: 4225-32. PMID 26592411 DOI: 10.1021/Ct400361K |
0.403 |
|
| 2013 |
Zhao H, Caflisch A. Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics. Bioorganic & Medicinal Chemistry Letters. 23: 5721-6. PMID 23993776 DOI: 10.1016/J.Bmcl.2013.08.009 |
0.379 |
|
| 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 |
0.386 |
|
| 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 |
0.387 |
|
| 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 |
0.481 |
|
| 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 |
0.336 |
|
| 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 |
0.748 |
|
| 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 |
0.737 |
|
| 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 |
0.389 |
|
| 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 |
0.305 |
|
| 2012 |
Zhou T, Caflisch A. Free Energy Guided Sampling. Journal of Chemical Theory and Computation. 8: 2134-40. PMID 26593843 DOI: 10.1021/Ct300147T |
0.346 |
|
| 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 |
0.335 |
|
| 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 |
0.309 |
|
| 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 |
0.344 |
|
| 2012 |
Zhou T, Caflisch A. Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric. Journal of Chemical Theory and Computation. 8: 2930-7. PMID 26592131 DOI: 10.1021/Ct3003145 |
0.408 |
|
| 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 |
0.408 |
|
| 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 |
0.391 |
|
| 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 |
0.374 |
|
| 2012 |
Steiner S, Caflisch A. Peptide binding to the PDZ3 domain by conformational selection. Proteins. 80: 2562-72. PMID 22753014 DOI: 10.1002/Prot.24137 |
0.429 |
|
| 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 |
0.359 |
|
| 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. PMID 22488806 DOI: 10.1002/Prot.24088 |
0.32 |
|
| 2012 |
Caflisch A, Hamm P. Complexity in Protein Folding: Simulation Meets Experiment Current Physical Chemistry. 2: 4-11. DOI: 10.5167/Uzh-65543 |
0.371 |
|
| 2011 |
Friedman R, Caflisch A. Surfactant effects on amyloid aggregation kinetics. Journal of Molecular Biology. 414: 303-12. PMID 22019473 DOI: 10.1016/J.Jmb.2011.10.011 |
0.367 |
|
| 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 |
0.766 |
|
| 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 |
0.592 |
|
| 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 |
0.677 |
|
| 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 |
0.747 |
|
| 2011 |
Ganesan R, Jelakovic S, Mittl PR, Caflisch A, Grütter MG. In silico identification and crystal structure validation of caspase-3 inhibitors without a P1 aspartic acid moiety. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 67: 842-50. PMID 21821879 DOI: 10.1107/S1744309111018604 |
0.366 |
|
| 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 |
0.388 |
|
| 2011 |
Scalco R, Caflisch A. Equilibrium distribution from distributed computing (simulations of protein folding). The Journal of Physical Chemistry. B. 115: 6358-65. PMID 21517045 DOI: 10.1021/Jp2014918 |
0.323 |
|
| 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 |
0.407 |
|
| 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 |
0.329 |
|
| 2010 |
Schuetz P, Wuttke R, Schuler B, Caflisch A. Free energy surfaces from single-distance information. The Journal of Physical Chemistry. B. 114: 15227-35. PMID 20964427 DOI: 10.1021/Jp1053698 |
0.36 |
|
| 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 |
0.315 |
|
| 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 |
0.385 |
|
| 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 |
0.736 |
|
| 2010 |
Zhou T, Caflisch A. High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors. Chemmedchem. 5: 1007-14. PMID 20540063 DOI: 10.1002/Cmdc.201000085 |
0.401 |
|
| 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 |
0.579 |
|
| 2010 |
Paoli B, Pellarin R, Caflisch A. Slow folding of cross-linked alpha-helical peptides due to steric hindrance. The Journal of Physical Chemistry. B. 114: 2023-7. PMID 20088553 DOI: 10.1021/Jp910216J |
0.335 |
|
| 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 |
0.354 |
|
| 2010 |
Zhou T, Huang D, Caflisch A. Quantum mechanical methods for drug design. Current Topics in Medicinal Chemistry. 10: 33-45. PMID 19929831 DOI: 10.2174/156802610790232242 |
0.355 |
|
| 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 |
0.376 |
|
| 2010 |
Magno A, Caflisch A, Pellarin R. Crowding Effects on Amyloid Aggregation Kinetics The Journal of Physical Chemistry Letters. 1: 3027-3032. DOI: 10.1021/Jz100967Z |
0.351 |
|
| 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 |
0.38 |
|
| 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 |
0.348 |
|
| 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 |
0.353 |
|
| 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 |
0.404 |
|
| 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 |
0.42 |
|
| 2009 |
Friedman R, Caflisch A. Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring. Chemmedchem. 4: 1317-26. PMID 19472268 DOI: 10.1002/Cmdc.200900078 |
0.386 |
|
| 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 |
0.752 |
|
| 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 |
0.307 |
|
| 2009 |
Ekonomiuk D, Caflisch A. Activation of the West Nile virus NS3 protease: molecular dynamics evidence for a conformational selection mechanism. Protein Science : a Publication of the Protein Society. 18: 1003-11. PMID 19388022 DOI: 10.1002/Pro.110 |
0.405 |
|
| 2009 |
Muff S, Caflisch A. Identification of the protein folding transition state from molecular dynamics trajectories. The Journal of Chemical Physics. 130: 125104. PMID 19334897 DOI: 10.1063/1.3099705 |
0.38 |
|
| 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 |
0.743 |
|
| 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 |
0.365 |
|
| 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 |
0.353 |
|
| 2009 |
Friedman R, Pellarin R, Caflisch A. Soluble Protofibrils as Metastable Intermediates in Simulations of Amyloid Fibril Degradation Induced by Lipid Vesicles The Journal of Physical Chemistry Letters. 1: 471-474. DOI: 10.1021/Jz900318T |
0.301 |
|
| 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 |
0.657 |
|
| 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 |
0.345 |
|
| 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 |
0.477 |
|
| 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 |
0.338 |
|
| 2008 |
Friedman R, Caflisch A. Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis. Proteins. 73: 814-27. PMID 18498105 DOI: 10.1002/Prot.22105 |
0.383 |
|
| 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 |
0.674 |
|
| 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 |
0.4 |
|
| 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 |
0.634 |
|
| 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 |
0.396 |
|
| 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 |
0.392 |
|
| 2008 |
Haberthür U, Caflisch A. FACTS: Fast analytical continuum treatment of solvation. Journal of Computational Chemistry. 29: 701-15. PMID 17918282 DOI: 10.1002/Jcc.20832 |
0.373 |
|
| 2008 |
Muff S, Caflisch A. Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein. Proteins. 70: 1185-95. PMID 17847092 DOI: 10.1002/Prot.21565 |
0.366 |
|
| 2007 |
Pellarin R, Guarnera E, Caflisch A. Pathways and intermediates of amyloid fibril formation. Journal of Molecular Biology. 374: 917-24. PMID 18028943 DOI: 10.1016/J.Jmb.2007.09.090 |
0.337 |
|
| 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 |
0.571 |
|
| 2007 |
Friedman R, Caflisch A. The protonation state of the catalytic aspartates in plasmepsin II. Febs Letters. 581: 4120-4. PMID 17689534 DOI: 10.1016/J.Febslet.2007.07.033 |
0.322 |
|
| 2007 |
Gorfe AA, Caflisch A. Ser170 controls the conformational multiplicity of the loop 166-175 in prion proteins: implication for conversion and species barrier. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 21: 3279-87. PMID 17522379 DOI: 10.1096/Fj.07-8292Com |
0.34 |
|
| 2007 |
Tartaglia GG, Caflisch A. Computational analysis of the S. cerevisiae proteome reveals the function and cellular localization of the least and most amyloidogenic proteins. Proteins. 68: 273-8. PMID 17407164 DOI: 10.1002/Prot.21427 |
0.356 |
|
| 2007 |
Gfeller D, De Los Rios P, Caflisch A, Rao F. Complex network analysis of free-energy landscapes. Proceedings of the National Academy of Sciences of the United States of America. 104: 1817-22. PMID 17267610 DOI: 10.1073/Pnas.0608099104 |
0.301 |
|
| 2007 |
Rao F, Settanni G, Guarnera E, Caflisch A. Estimation of protein folding probability from equilibrium simulations. The Journal of Chemical Physics. 122: 184901. PMID 15918759 DOI: 10.1063/1.1893753 |
0.379 |
|
| 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 |
0.675 |
|
| 2006 |
Rao F, Settanni G, Caflisch A. Estimation of folding probabilities and phi values from molecular dynamics simulations of reversible Peptide folding. Methods in Molecular Biology (Clifton, N.J.). 350: 225-49. PMID 16957326 DOI: 10.1385/1-59745-189-4:225 |
0.399 |
|
| 2006 |
Caflisch A. Computational models for the prediction of polypeptide aggregation propensity. Current Opinion in Chemical Biology. 10: 437-44. PMID 16880001 DOI: 10.1016/J.Cbpa.2006.07.009 |
0.373 |
|
| 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 |
0.323 |
|
| 2006 |
Pellarin R, Caflisch A. Interpreting the aggregation kinetics of amyloid peptides. Journal of Molecular Biology. 360: 882-92. PMID 16797587 DOI: 10.1016/J.Jmb.2006.05.033 |
0.37 |
|
| 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 |
0.751 |
|
| 2006 |
Interlandi G, Settanni G, Caflisch A. Unfolding transition state and intermediates of the tumor suppressor p16INK4a investigated by molecular dynamics simulations. Proteins. 64: 178-92. PMID 16596641 DOI: 10.1002/Prot.20953 |
0.39 |
|
| 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 |
0.601 |
|
| 2006 |
Caflisch A. Network and graph analyses of folding free energy surfaces. Current Opinion in Structural Biology. 16: 71-8. PMID 16413772 DOI: 10.1016/J.Sbi.2006.01.002 |
0.358 |
|
| 2006 |
Gorfe AA, Caflisch A. Functional plasticity in the substrate binding site of beta-secretase. Structure (London, England : 1993). 13: 1487-98. PMID 16216580 DOI: 10.1016/J.Str.2005.06.015 |
0.413 |
|
| 2005 |
Tartaglia GG, Cavalli A, Pellarin R, Caflisch A. Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences. Protein Science : a Publication of the Protein Society. 14: 2723-34. PMID 16195556 DOI: 10.1110/Ps.051471205 |
0.339 |
|
| 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 |
0.302 |
|
| 2005 |
Tartaglia GG, Pellarin R, Cavalli A, Caflisch A. Organism complexity anti-correlates with proteomic beta-aggregation propensity. Protein Science : a Publication of the Protein Society. 14: 2735-40. PMID 16155201 DOI: 10.1110/Ps.051473805 |
0.318 |
|
| 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 |
0.723 |
|
| 2005 |
Böckmann RA, Caflisch A. Spontaneous formation of detergent micelles around the outer membrane protein OmpX. Biophysical Journal. 88: 3191-204. PMID 15749771 DOI: 10.1529/Biophysj.105.060426 |
0.384 |
|
| 2005 |
Settanni G, Rao F, Caflisch A. Phi-value analysis by molecular dynamics simulations of reversible folding. Proceedings of the National Academy of Sciences of the United States of America. 102: 628-33. PMID 15644439 DOI: 10.1073/Pnas.0406754102 |
0.364 |
|
| 2005 |
Gorfe AA, Pellarin R, Caflisch A. Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations. Journal of the American Chemical Society. 126: 15277-86. PMID 15548025 DOI: 10.1021/Ja046607N |
0.354 |
|
| 2005 |
Caflisch A. Protein folding: simple models for a complex process. Structure (London, England : 1993). 12: 1750-2. PMID 15458624 DOI: 10.1016/J.Str.2004.09.001 |
0.315 |
|
| 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 |
0.59 |
|
| 2004 |
Huang D, Caflisch A. Efficient evaluation of binding free energy using continuum electrostatics solvation. Journal of Medicinal Chemistry. 47: 5791-7. PMID 15509178 DOI: 10.1021/Jm049726M |
0.344 |
|
| 2004 |
Rao F, Caflisch A. The protein folding network. Journal of Molecular Biology. 342: 299-306. PMID 15313625 DOI: 10.1016/J.Jmb.2004.06.063 |
0.328 |
|
| 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 |
0.38 |
|
| 2004 |
Tartaglia GG, Cavalli A, Pellarin R, Caflisch A. The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates. Protein Science : a Publication of the Protein Society. 13: 1939-41. PMID 15169952 DOI: 10.1110/Ps.04663504 |
0.35 |
|
| 2004 |
Gorfe AA, Caflisch A, Jelesarov I. The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: a molecular dynamics analysis. Journal of Molecular Recognition : Jmr. 17: 120-31. PMID 15027032 DOI: 10.1002/Jmr.658 |
0.384 |
|
| 2004 |
Settanni G, Gsponer J, Caflisch A. Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations. Biophysical Journal. 86: 1691-701. PMID 14990497 DOI: 10.1016/S0006-3495(04)74238-1 |
0.365 |
|
| 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 |
0.721 |
|
| 2004 |
Haberthür U, Majeux N, Werner P, Caflisch A. Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution. Journal of Computational Chemistry. 24: 1936-49. PMID 14515376 DOI: 10.1002/Jcc.10317 |
0.305 |
|
| 2004 |
Caflisch A. Folding for binding or binding for folding? Trends in Biotechnology. 21: 423-5. PMID 14512226 DOI: 10.1016/S0167-7799(03)00208-7 |
0.368 |
|
| 2004 |
Cavalli A, Haberthür U, Paci E, Caflisch A. Fast protein folding on downhill energy landscape. Protein Science : a Publication of the Protein Society. 12: 1801-3. PMID 12876329 DOI: 10.1110/Ps.0366103 |
0.382 |
|
| 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 |
0.537 |
|
| 2003 |
Gsponer J, Haberthür U, Caflisch A. The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proceedings of the National Academy of Sciences of the United States of America. 100: 5154-9. PMID 12700355 DOI: 10.1073/Pnas.0835307100 |
0.405 |
|
| 2003 |
Werner P, Caflisch A. A sphere-based model for the electrostatics of globular proteins. Journal of the American Chemical Society. 125: 4600-8. PMID 12683832 DOI: 10.1021/Ja021093I |
0.309 |
|
| 2003 |
Rao F, Caflisch A. Replica exchange molecular dynamics simulations of reversible folding The Journal of Chemical Physics. 119: 4035-4042. DOI: 10.1063/1.1591721 |
0.367 |
|
| 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 |
0.326 |
|
| 2003 |
Settanni G, Gsponer J, Caflisch A. 488.1-Pos Board # B29.1 – Formation of the Folding Nucleus of src-SH3 Domain from Denatured Conformations Investigated Through Biased Molecular Dynamics Simulations Biophysical Journal. 84: 3488. DOI: 10.1016/S0006-3495(03)70113-1 |
0.315 |
|
| 2002 |
Gsponer J, Caflisch A. Molecular dynamics simulations of protein folding from the transition state. Proceedings of the National Academy of Sciences of the United States of America. 99: 6719-24. PMID 11983864 DOI: 10.1073/Pnas.092686399 |
0.378 |
|
| 2002 |
Cavalli A, Ferrara P, Caflisch A. Weak temperature dependence of the free energy surface and folding pathways of structured peptides. Proteins. 47: 305-14. PMID 11948784 DOI: 10.1002/Prot.10041 |
0.338 |
|
| 2002 |
Budin N, Ahmed S, Majeux N, Caflisch A. An evolutionary approach for structure-based design of natural and non-natural peptidic ligands. Combinatorial Chemistry & High Throughput Screening. 4: 661-73. PMID 11812261 DOI: 10.2174/1386207013330652 |
0.397 |
|
| 2002 |
Gsponer J, Ferrara P, Caflisch A. Flexibility of the murine prion protein and its Asp178Asn mutant investigated by molecular dynamics simulations. Journal of Molecular Graphics & Modelling. 20: 169-82. PMID 11775003 DOI: 10.1016/S1093-3263(01)00117-6 |
0.37 |
|
| 2002 |
Gorfe AA, Ferrara P, Caflisch A, Marti DN, Bosshard HR, Jelesarov I. Calculation of protein ionization equilibria with conformational sampling: pK(a) of a model leucine zipper, GCN4 and barnase. Proteins. 46: 41-60. PMID 11746702 DOI: 10.1002/Prot.10027 |
0.375 |
|
| 2002 |
Ferrara P, Apostolakis J, Caflisch A. Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins. 46: 24-33. PMID 11746700 DOI: 10.1002/Prot.10001 |
0.389 |
|
| 2002 |
Budin N, Majeux N, Caflisch A. Fragment-Based flexible ligand docking by evolutionary optimization. Biological Chemistry. 382: 1365-72. PMID 11688719 DOI: 10.1515/Bc.2001.168 |
0.381 |
|
| 2002 |
Ahmed S, Majeux N, Caflisch A. Hydrophobicity and functionality maps of farnesyltransferase. Journal of Molecular Graphics & Modelling. 19: 307-17, 380-7. PMID 11449569 DOI: 10.1016/S1093-3263(00)00075-9 |
0.371 |
|
| 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 |
0.481 |
|
| 2001 |
Gsponer J, Caflisch A. Role of native topology investigated by multiple unfolding simulations of four SH3 domains. Journal of Molecular Biology. 309: 285-98. PMID 11491296 DOI: 10.1006/Jmbi.2001.4552 |
0.352 |
|
| 2001 |
Ferrara P, Caflisch A. Native topology or specific interactions: what is more important for protein folding? Journal of Molecular Biology. 306: 837-50. PMID 11243792 DOI: 10.1006/Jmbi.2000.4400 |
0.369 |
|
| 2001 |
Majeux N, Scarsi M, Caflisch A. Efficient electrostatic solvation model for protein-fragment docking. Proteins. 42: 256-68. PMID 11119650 DOI: 10.1002/1097-0134(20010201)42:2<256::Aid-Prot130>3.0.Co;2-4 |
0.42 |
|
| 2001 |
Budin N, Majeux N, Tenette-Souaille C, Caflisch A. Structure-based ligand design by a build-up approach and genetic algorithm search in conformational space Journal of Computational Chemistry. 22: 1956-1970. DOI: 10.1002/Jcc.1145 |
0.392 |
|
| 2000 |
Ferrara P, Caflisch A. Folding simulations of a three-stranded antiparallel beta -sheet peptide. Proceedings of the National Academy of Sciences of the United States of America. 97: 10780-5. PMID 10984515 DOI: 10.1073/Pnas.190324897 |
0.366 |
|
| 2000 |
Ferrara P, Apostolakis J, Caflisch A. Computer simulations of protein folding by targeted molecular dynamics. Proteins. 39: 252-60. PMID 10737947 DOI: 10.1002/(Sici)1097-0134(20000515)39:3<252::Aid-Prot80>3.0.Co;2-3 |
0.379 |
|
| 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 |
0.441 |
|
| 2000 |
Galzitskaya O, Caflisch A. Solution conformation of phakellistatin 8 investigated by molecular dynamics simulations. Journal of Molecular Graphics & Modelling. 17: 19-27. PMID 10660907 DOI: 10.1016/S1093-3263(99)00017-0 |
0.339 |
|
| 2000 |
Scarsi M, Majeux N, Caflisch A. Hydrophobicity at the surface of proteins. Proteins. 37: 565-75. PMID 10651272 DOI: 10.1002/(Sici)1097-0134(19991201)37:4<565::Aid-Prot7>3.0.Co;2-V |
0.377 |
|
| 2000 |
Ferrara P, Apostolakis J, Caflisch A. Targeted Molecular Dynamics Simulations of Protein Unfolding The Journal of Physical Chemistry B. 104: 4511-4518. DOI: 10.1021/Jp9943878 |
0.361 |
|
| 2000 |
Ferrara P, Apostolakis J, Caflisch A. Thermodynamics and Kinetics of Folding of Two Model Peptides Investigated by Molecular Dynamics Simulations The Journal of Physical Chemistry B. 104: 5000-5010. DOI: 10.1021/Jp994157T |
0.343 |
|
| 2000 |
Hiltpold A, Ferrara P, Gsponer J, Caflisch A. Free Energy Surface of the Helical Peptide Y(MEARA)6 The Journal of Physical Chemistry B. 104: 10080-10086. DOI: 10.1021/Jp002207K |
0.383 |
|
| 2000 |
Majeux N, Carsi M, Tenette-Souaille C, Caflisch A. Hydrophobicity maps and docking of molecular fragments with solvation Perspectives in Drug Discovery and Design. 20: 145-169. DOI: 10.1007/0-306-46883-2_9 |
0.39 |
|
| 1999 |
Majeux N, Scarsi M, Apostolakis J, Ehrhardt C, Caflisch A. Exhaustive docking of molecular fragments with electrostatic solvation. Proteins. 37: 88-105. PMID 10451553 DOI: 10.1002/(Sici)1097-0134(19991001)37:1<88::Aid-Prot9>3.0.Co;2-O |
0.426 |
|
| 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 |
0.517 |
|
| 1999 |
Apostolakis J, Ferrara P, Caflisch A. Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water The Journal of Chemical Physics. 110: 2099-2108. DOI: 10.1063/1.477819 |
0.333 |
|
| 1999 |
Scarsi M, Caflisch A. Comment on the validation of continuum electrostatics models Journal of Computational Chemistry. 20: 1533-1536. DOI: 10.1002/(Sici)1096-987X(19991115)20:14<1533::Aid-Jcc6>3.0.Co;2-3 |
0.308 |
|
| 1998 |
Apostolakis J, Pl�ckthun A, Caflisch A. Docking small ligands in flexible binding sites Journal of Computational Chemistry. 19: 21-37. DOI: 10.1002/(Sici)1096-987X(19980115)19:1<21::Aid-Jcc2>3.0.Co;2-0 |
0.387 |
|
| 1997 |
Caflisch A. Computational combinatorial ligand design: application to human alpha-thrombin. Journal of Computer-Aided Molecular Design. 10: 372-96. PMID 8951649 DOI: 10.1007/Bf00124471 |
0.416 |
|
| 1997 |
Scarsi M, Apostolakis J, Caflisch A. Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions The Journal of Physical Chemistry A. 101: 8098-8106. DOI: 10.1021/Jp9714227 |
0.302 |
|
| 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 |
0.54 |
|
| 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 |
0.504 |
|
| 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 |
0.484 |
|
| 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 |
0.499 |
|
| 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 |
0.513 |
|
| 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 |
0.526 |
|
| 1992 |
Caflisch A, Niederer P, Anliker M. Monte Carlo docking of oligopeptides to proteins. Proteins. 13: 223-30. PMID 1603811 DOI: 10.1002/Prot.340130305 |
0.626 |
|
| 1992 |
Caflisch A, Niederer P, Anliker M. Monte Carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space. Proteins. 14: 102-9. PMID 1409559 DOI: 10.1002/Prot.340140111 |
0.589 |
|
| 1991 |
Caflisch A, Kündig M, Lehareinger Y, Niederer P. Molecular graphics for protein folding simulations Journal of Molecular Graphics. 9: 65. DOI: 10.1016/0263-7855(91)80079-F |
0.549 |
|
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