ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions. - Andreas Vitalis; Rohit V. Pappu (J. Comput. Chem., 2009)

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)

An Improved and Parallel Version of a Scalable Algorithm for Analyzing Time Series Data. - Andreas Vitalis (CoRR, 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)

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)

Benchmarking the robustness of the correct identification of flexible 3D objects using common machine learning models. - Yang Zhang 108; Andreas Vitalis (Patterns, 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)