Amedeo Caflisch

33 papers A 1B 1Journal 31

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A FAIR-Compliant Management Solution for Molecular Simulation Trajectories. J. Chem. Inf. Model. Andreas Vitalis, Steffen Winkler, Yang Zhang, Julian Widmer, Amedeo Caflisch
2025	J	`jnl`	Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening. J. Comput. Chem. Andreas Vitalis, David Parker, Fabian Radler, Pablo A. Vargas-Rosales, Yang Zhang, Jean-Rémy Marchand, Amedeo Caflisch
2023	J	`jnl`	Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations. J. Chem. Inf. Model. Ioana M. Ilie, Claus Ehrhardt, Amedeo Caflisch, Gabriele Weitz-Schmidt
2023	J	`jnl`	Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors. J. Chem. Inf. Model. Raitis Bobrovs, Laura Drunka, Iveta Kanepe, Aigars Jirgensons, Amedeo Caflisch, Matteo Salvalaglio, Kristaps Jaudzems
2022	J	`jnl`	Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein. J. Chem. Inf. Model. Ilaria Salutari, Amedeo Caflisch
2020	J	`jnl`	An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules. J. Chem. Inf. Model. Jean-Rémy Marchand, Tim Knehans, Amedeo Caflisch, Andreas Vitalis
2020	J	`jnl`	Assessment of the Fragment Docking Program SEED. J. Chem. Inf. Model. Kenneth Goossens, Berthold Wroblowski, Cassiano Langini, Herman van Vlijmen, Amedeo Caflisch, Hans De Winter
2020	J	`jnl`	Structural and Dynamic Insights into Redundant Function of YTHDF Proteins. J. Chem. Inf. Model. Yaozong Li, Rajiv K. Bedi, Elena V. Moroz-Omori, Amedeo Caflisch
2018	J	`jnl`	In Silico Identification of JMJD3 Demethylase Inhibitors. J. Chem. Inf. Model. Carmen Esposito, L. Wiedmer, Amedeo Caflisch
2017	J	`jnl`	Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. J. Chem. Inf. Model. Jean-Rémy Marchand, Andrea Dalle Vedove, Graziano Lolli, Amedeo Caflisch
2014	J	`jnl`	ALMOST: An all atom molecular simulation toolkit for protein structure determination. J. Comput. Chem. Biao Fu, Aleksandr B. Sahakyan, Carlo Camilloni, Gian Gaetano Tartaglia, Emanuele Paci, Amedeo Caflisch, Michele Vendruscolo, Andrea Cavalli
2014	J	`jnl`	Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design. J. Chem. Inf. Model. Yuri Pevzner, Emilie Frugier, Vinushka Schalk, Amedeo Caflisch, H. Lee Woodcock III
2013	J	`jnl`	A scalable algorithm to order and annotate continuous observations reveals the metastable states visited by dynamical systems. Comput. Phys. Commun. Nicolas Blöchliger, Andreas Vitalis, Amedeo Caflisch
2011	J	`jnl`	The Free Energy Landscape of Small Molecule Unbinding. PLoS Comput. Biol. Danzhi Huang, Amedeo Caflisch
2011	J	`jnl`	Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. J. Comput. Chem. Michele Seeber, Angelo Felline, Francesco Raimondi, Stefanie Muff, Ran Friedman, Francesco Rao, Amedeo Caflisch, Francesca Fanelli
2010	J	`jnl`	Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis. Bioinform. Danzhi Huang, Ting Zhou, Karine Lafleur, Cristina Nevado, Amedeo Caflisch
2009	J	`jnl`	CHARMM: The biomolecular simulation program. J. Comput. Chem. 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, Victor 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
2009	J	`jnl`	Data Management System for Distributed Virtual Screening. J. Chem. Inf. Model. Ting Zhou, Amedeo Caflisch
2008	J	`jnl`	FACTS: Fast analytical continuum treatment of solvation. J. Comput. Chem. Urs Haberthür, Amedeo Caflisch
2008	J	`jnl`	Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization. J. Chem. Inf. Model. Fabian Dey, Amedeo Caflisch
2008	J	`jnl`	Multistep greedy algorithm identifies community structure in real-world and computer-generated networks CoRR Philipp Schuetz, Amedeo Caflisch
2007	J	`jnl`	Efficient Modularity Optimization: Multi-Step Greedy Algorithm and Vertex Mover Refinement CoRR Philipp Schuetz, Amedeo Caflisch
2007	J	`jnl`	Wordom: a program for efficient analysis of molecular dynamics simulations. Bioinform. Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch
2004	J	`jnl`	Automated docking of highly flexible ligands by genetic algorithms: A critical assessment. J. Comput. Chem. Marco Cecchini, Peter Kolb, Nicolas Majeux, Amedeo Caflisch
2003	B	`conf`	Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform. CCGRID Bennet Uk, Michela Taufer, Thomas Stricker, Giovanni Settanni, Andrea Cavalli, Amedeo Caflisch
2003	J	`jnl`	Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution. J. Comput. Chem. Urs Haberthür, Nicolas Majeux, Philipp Werner, Amedeo Caflisch
2002	A	`conf`	Performance Characterization of a Molecular Dynamics Code on PC Clusters: Is There Any Easy Parallelism in CHARMM?. IPDPS Michela Taufer, Egon Perathoner, Andrea Cavalli, Amedeo Caflisch, Thomas Stricker
2001	J	`jnl`	Structure-based ligand design by a build-up approach and genetic algorithm search in conformational space. J. Comput. Chem. Nicolas Budin, Nicolas Majeux, Catherine Tenette-Souaille, Amedeo Caflisch
2000	J	`jnl`	Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach. J. Comput. Aided Mol. Des. Amedeo Caflisch, Hans J. Schramm, Martin Karplus
1999	J	`jnl`	Comment on the validation of continuum electrostatics models. J. Comput. Chem. Marco Scarsi, Amedeo Caflisch
1998	J	`jnl`	Docking small ligands in flexible binding sites. J. Comput. Chem. Joannis Apostolakis, Andreas Plückthun, Amedeo Caflisch
1997	J	`jnl`	Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP - substrate complex. J. Comput. Chem. Amedeo Caflisch, Stefan Fischer, Martin Karplus
1996	J	`jnl`	Computational combinatorial ligand design: Application to human alpha-thrombin. J. Comput. Aided Mol. Des. Amedeo Caflisch