Computational combinatorial ligand design: Application to human alpha-thrombin. - Amedeo Caflisch (J. Comput. Aided Mol. Des., 1996)

Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP - substrate complex. - Amedeo Caflisch; Stefan Fischer 004; Martin Karplus (J. Comput. Chem., 1997)

Docking small ligands in flexible binding sites. - Joannis Apostolakis; Andreas Plückthun; Amedeo Caflisch (J. Comput. Chem., 1998)

Comment on the validation of continuum electrostatics models. - Marco Scarsi; Amedeo Caflisch (J. Comput. Chem., 1999)

Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach. - Amedeo Caflisch; Hans J. Schramm; Martin Karplus (J. Comput. Aided Mol. Des., 2000)

Structure-based ligand design by a build-up approach and genetic algorithm search in conformational space. - Nicolas Budin; Nicolas Majeux; Catherine Tenette-Souaille; Amedeo Caflisch (J. Comput. Chem., 2001)

Performance Characterization of a Molecular Dynamics Code on PC Clusters: Is There Any Easy Parallelism in CHARMM?. - Michela Taufer; Egon Perathoner; Andrea Cavalli; Amedeo Caflisch; Thomas Stricker (IPDPS, 2002)

Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform. - Bennet Uk; Michela Taufer; Thomas Stricker; Giovanni Settanni; Andrea Cavalli; Amedeo Caflisch (CCGRID, 2003)

Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution. - Urs Haberthür; Nicolas Majeux; Philipp Werner; Amedeo Caflisch (J. Comput. Chem., 2003)

Automated docking of highly flexible ligands by genetic algorithms: A critical assessment. - Marco Cecchini; Peter Kolb; Nicolas Majeux; Amedeo Caflisch (J. Comput. Chem., 2004)

Wordom: a program for efficient analysis of molecular dynamics simulations. - Michele Seeber; Marco Cecchini; Francesco Rao; Giovanni Settanni; Amedeo Caflisch (Bioinform., 2007)

Efficient Modularity Optimization: Multi-Step Greedy Algorithm and Vertex Mover Refinement - Philipp Schuetz; Amedeo Caflisch (CoRR, 2007)

Multistep greedy algorithm identifies community structure in real-world and computer-generated networks - Philipp Schuetz; Amedeo Caflisch (CoRR, 2008)

FACTS: Fast analytical continuum treatment of solvation. - Urs Haberthür; Amedeo Caflisch (J. Comput. Chem., 2008)

Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization. - Fabian Dey; Amedeo Caflisch (J. Chem. Inf. Model., 2008)

CHARMM: The biomolecular simulation program. - 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; et al. (J. Comput. Chem., 2009)

Data Management System for Distributed Virtual Screening. - Ting Zhou; Amedeo Caflisch (J. Chem. Inf. Model., 2009)

Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis. - Danzhi Huang; Ting Zhou; Karine Lafleur; Cristina Nevado; Amedeo Caflisch (Bioinform., 2010)

Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. - Michele Seeber; Angelo Felline; Francesco Raimondi 001; Stefanie Muff; Ran Friedman; Francesco Rao; Amedeo Caflisch; Francesca Fanelli (J. Comput. Chem., 2011)

The Free Energy Landscape of Small Molecule Unbinding. - Danzhi Huang; Amedeo Caflisch (PLoS Comput. Biol., 2011)

A scalable algorithm to order and annotate continuous observations reveals the metastable states visited by dynamical systems. - Nicolas Blöchliger; Andreas Vitalis; Amedeo Caflisch (Comput. Phys. Commun., 2013)

ALMOST: An all atom molecular simulation toolkit for protein structure determination. - Biao Fu; Aleksandr B. Sahakyan; Carlo Camilloni; Gian Gaetano Tartaglia; Emanuele Paci; Amedeo Caflisch; Michele Vendruscolo; Andrea Cavalli (J. Comput. Chem., 2014)

Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design. - Yuri Pevzner; Emilie Frugier; Vinushka Schalk; Amedeo Caflisch; H. Lee Woodcock III (J. Chem. Inf. Model., 2014)

Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. - Jean-Rémy Marchand; Andrea Dalle Vedove; Graziano Lolli; Amedeo Caflisch (J. Chem. Inf. Model., 2017)

In Silico Identification of JMJD3 Demethylase Inhibitors. - Carmen Esposito; L. Wiedmer; Amedeo Caflisch (J. Chem. Inf. Model., 2018)

Assessment of the Fragment Docking Program SEED. - Kenneth Goossens; Berthold Wroblowski; Cassiano Langini; Herman van Vlijmen; Amedeo Caflisch; Hans De Winter (J. Chem. Inf. Model., 2020)

Structural and Dynamic Insights into Redundant Function of YTHDF Proteins. - Yaozong Li; Rajiv K. Bedi; Elena V. Moroz-Omori; Amedeo Caflisch (J. Chem. Inf. Model., 2020)

An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules. - Jean-Rémy Marchand; Tim Knehans; Amedeo Caflisch; Andreas Vitalis (J. Chem. Inf. Model., 2020)

Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein. - Ilaria Salutari; Amedeo Caflisch (J. Chem. Inf. Model., 2022)

Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations. - Ioana M. Ilie; Claus Ehrhardt; Amedeo Caflisch; Gabriele Weitz-Schmidt (J. Chem. Inf. Model., 2023)

Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors. - Raitis Bobrovs; Laura Drunka; Iveta Kanepe; Aigars Jirgensons; Amedeo Caflisch; Matteo Salvalaglio; Kristaps Jaudzems (J. Chem. Inf. Model., 2023)

A FAIR-Compliant Management Solution for Molecular Simulation Trajectories. - Andreas Vitalis; Steffen Winkler; Yang Zhang 108; Julian Widmer; Amedeo Caflisch (J. Chem. Inf. Model., 2025)

Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening. - Andreas Vitalis; David Parker; Fabian Radler; Pablo A. Vargas-Rosales; Yang Zhang 108; Jean-Rémy Marchand; Amedeo Caflisch (J. Comput. Chem., 2025)