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ORCIDAmedeo Caflisch
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2020 – today
- 2020
[j23]Kenneth Goossens, Berthold Wroblowski, Cassiano Langini, Herman van Vlijmen, Amedeo Caflisch
, Hans De Winter:
Assessment of the Fragment Docking Program SEED. J. Chem. Inf. Model. 60(10): 4881-4893 (2020)- [j22]Jean-Rémy Marchand, Tim Knehans, Amedeo Caflisch, Andreas Vitalis:
An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules. J. Chem. Inf. Model. 60(10): 5188-5202 (2020) - [j21]Yaozong Li, Rajiv K. Bedi, Elena V. Moroz-Omori, Amedeo Caflisch:
Structural and Dynamic Insights into Redundant Function of YTHDF Proteins. J. Chem. Inf. Model. 60(12): 5932-5935 (2020)
2010 – 2019
- 2018
- [j20]Carmen Esposito, L. Wiedmer, Amedeo Caflisch:
In Silico Identification of JMJD3 Demethylase Inhibitors. J. Chem. Inf. Model. 58(10): 2151-2163 (2018) - 2014
- [j19]Biao Fu, Aleksandr B. Sahakyan, Carlo Camilloni, Gian Gaetano Tartaglia, Emanuele Paci, Amedeo Caflisch, Michele Vendruscolo, Andrea Cavalli:
ALMOST: An all atom molecular simulation toolkit for protein structure determination. J. Comput. Chem. 35(14): 1101-1105 (2014) - [j18]Yuri Pevzner, Emilie Frugier, Vinushka Schalk, Amedeo Caflisch, H. Lee Woodcock III:
Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design. J. Chem. Inf. Model. 54(9): 2612-2620 (2014) - 2013
- [j17]Nicolas Blöchliger, Andreas Vitalis, Amedeo Caflisch:
A scalable algorithm to order and annotate continuous observations reveals the metastable states visited by dynamical systems. Comput. Phys. Commun. 184(11): 2446-2453 (2013) - 2011
- [j16]Michele Seeber, Angelo Felline, Francesco Raimondi, Stefanie Muff, Ran Friedman, Francesco Rao, Amedeo Caflisch, Francesca Fanelli:
Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. J. Comput. Chem. 32(6): 1183-1194 (2011) - [j15]Danzhi Huang, Amedeo Caflisch:
The Free Energy Landscape of Small Molecule Unbinding. PLoS Comput. Biol. 7(2) (2011) - 2010
- [j14]Danzhi Huang, Ting Zhou, Karine Lafleur, Cristina Nevado, Amedeo Caflisch:
Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis. Bioinform. 26(2): 198-204 (2010)
2000 – 2009
- 2009
- [j13]Bernard R. Brooks, Charles L. Brooks III, Alexander D. MacKerell Jr., Lennart Nilsson, Robert J. Petrella, Benoît Roux, Y. Won, G. Archontis, Christian Bartels, Stefan Boresch, Amedeo Caflisch, Leo S. D. Caves, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, V. Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus:
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30(10): 1545-1614 (2009) - [j12]Ting Zhou, Amedeo Caflisch:
Data Management System for Distributed Virtual Screening. J. Chem. Inf. Model. 49(1): 145-152 (2009) - 2008
- [j11]Urs Haberthür, Amedeo Caflisch:
FACTS: Fast analytical continuum treatment of solvation. J. Comput. Chem. 29(5): 701-715 (2008) - [j10]Fabian Dey, Amedeo Caflisch:
Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization. J. Chem. Inf. Model. 48(3): 679-690 (2008) - [i2]Philipp Schuetz, Amedeo Caflisch:
Multistep greedy algorithm identifies community structure in real-world and computer-generated networks. CoRR abs/0809.4398 (2008) - 2007
- [j9]Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch:
Wordom: a program for efficient analysis of molecular dynamics simulations. Bioinform. 23(19): 2625-2627 (2007) - [i1]Philipp Schuetz, Amedeo Caflisch:
Efficient Modularity Optimization: Multi-Step Greedy Algorithm and Vertex Mover Refinement. CoRR abs/0712.1163 (2007) - 2004
- [j8]Marco Cecchini, Peter Kolb, Nicolas Majeux, Amedeo Caflisch:
Automated docking of highly flexible ligands by genetic algorithms: A critical assessment. J. Comput. Chem. 25(3): 412-422 (2004) - 2003
- [j7]Urs Haberthür, Nicolas Majeux, Philipp Werner, Amedeo Caflisch:
Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution. J. Comput. Chem. 24(15): 1936-1949 (2003) - [c2]Bennet Uk, Michela Taufer, Thomas Stricker, Giovanni Settanni, Andrea Cavalli, Amedeo Caflisch:
Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform. CCGRID 2003: 240-247 - 2002
- [c1]Michela Taufer, Egon Perathoner, Andrea Cavalli, Amedeo Caflisch, Thomas Stricker:
Performance Characterization of a Molecular Dynamics Code on PC Clusters: Is There Any Easy Parallelism in CHARMM?. IPDPS 2002 - 2001
- [j6]Nicolas Budin, Nicolas Majeux, Catherine Tenette-Souaille, Amedeo Caflisch:
Structure-based ligand design by a build-up approach and genetic algorithm search in conformational space. J. Comput. Chem. 22(16): 1956-1970 (2001) - 2000
- [j5]Amedeo Caflisch, Hans J. Schramm, Martin Karplus:
Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach. J. Comput. Aided Mol. Des. 14(2): 161-179 (2000)
1990 – 1999
- 1999
- [j4]Marco Scarsi, Amedeo Caflisch:
Comment on the validation of continuum electrostatics models. J. Comput. Chem. 20(14): 1533-1536 (1999) - 1998
- [j3]Joannis Apostolakis, Andreas Plückthun, Amedeo Caflisch:
Docking small ligands in flexible binding sites. J. Comput. Chem. 19(1): 21-37 (1998) - 1997
- [j2]Amedeo Caflisch, Stefan Fischer, Martin Karplus:
Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP - substrate complex. J. Comput. Chem. 18(6): 723-743 (1997) - 1996
- [j1]Amedeo Caflisch:
Computational combinatorial ligand design: Application to human alpha-thrombin. J. Comput. Aided Mol. Des. 10(5): 372-396 (1996)
Coauthor Index
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