Amedeo Caflisch

Publication Activity (10 Years)

Years Active: 1996-2023
Publications (10 Years): 8

Top Topics

Protein Structural

Seeded Region Growing

Top Venues

J. Chem. Inf. Model.

J. Comput. Chem.

Publications

Raitis Bobrovs, Laura Drunka, Iveta Kanepe, Aigars Jirgensons, Amedeo Caflisch, Matteo Salvalaglio, Kristaps Jaudzems
Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors. J. Chem. Inf. Model. 63 (21) (2023)
Ioana M. Ilie, Claus Ehrhardt, Amedeo Caflisch, Gabriele Weitz-Schmidt
Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations. J. Chem. Inf. Model. 63 (12) (2023)
Ilaria Salutari, Amedeo Caflisch
Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein. J. Chem. Inf. Model. 62 (4) (2022)
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) (2020)
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) (2020)
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) (2020)
Carmen Esposito, L. Wiedmer, Amedeo Caflisch
In Silico Identification of JMJD3 Demethylase Inhibitors. J. Chem. Inf. Model. 58 (10) (2018)
Jean-Rémy Marchand, Andrea Dalle Vedove, Graziano Lolli, Amedeo Caflisch
Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. J. Chem. Inf. Model. 57 (10) (2017)
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) (2014)
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) (2014)
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) (2013)
Danzhi Huang, Amedeo Caflisch
The Free Energy Landscape of Small Molecule Unbinding. PLoS Comput. Biol. 7 (2) (2011)
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) (2011)
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) (2010)
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) (2009)
Ting Zhou, Amedeo Caflisch
Data Management System for Distributed Virtual Screening. J. Chem. Inf. Model. 49 (1) (2009)
Fabian Dey, Amedeo Caflisch
Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization. J. Chem. Inf. Model. 48 (3) (2008)
Urs Haberthür, Amedeo Caflisch
FACTS: Fast analytical continuum treatment of solvation. J. Comput. Chem. 29 (5) (2008)
Philipp Schuetz, Amedeo Caflisch
Multistep greedy algorithm identifies community structure in real-world and computer-generated networks CoRR (2008)
Philipp Schuetz, Amedeo Caflisch
Efficient Modularity Optimization: Multi-Step Greedy Algorithm and Vertex Mover Refinement CoRR (2007)
Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch
Wordom: a program for efficient analysis of molecular dynamics simulations. Bioinform. 23 (19) (2007)
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) (2004)
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)
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) (2003)
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)
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) (2001)
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) (2000)
Marco Scarsi, Amedeo Caflisch
Comment on the validation of continuum electrostatics models. J. Comput. Chem. 20 (14) (1999)
Joannis Apostolakis, Andreas Plückthun, Amedeo Caflisch
Docking small ligands in flexible binding sites. J. Comput. Chem. 19 (1) (1998)
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) (1997)
Amedeo Caflisch
Computational combinatorial ligand design: Application to human alpha-thrombin. J. Comput. Aided Mol. Des. 10 (5) (1996)