Multitemplate Alignment Method for the Development of a Reliable 3D-QSAR Model for the Analysis of MMP3 Inhibitors. - Tiziano Tuccinardi; Gabriella Ortore; M. Amélia Santos; Sérgio M. Marques; Elisa Nuti; Armando Rossello; Adriano Martinelli (J. Chem. Inf. Model., 2009)

Watergate: Visual Exploration of Water Trajectories in Protein Dynamics. - Viktor Vad; Jan Byska; Adam Jurcík; Ivan Viola; M. Eduard Gröller; Helwig Hauser; Sérgio M. Marques; Jirí Damborský; Barbora Kozlíková (VCBM, 2017)

Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling. - Sérgio M. Marques; Zuzana Dunajova; Zbynek Prokop; Radka Chaloupkova; Jan Brezovsky; Jirí Damborský (J. Chem. Inf. Model., 2017)

CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories. - Adam Jurcík; David Bednar; Jan Byska; Sérgio M. Marques; Katarína Furmanová; Lukas Daniel; Piia Kokkonen; Jan Brezovsky; Ondrej Strnad; Jan Stourac; Antonín Pavelka; Martin Manak; et al. (Bioinform., 2018)

CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. - Ondrej Vavra; Jiri Filipovic; Jan Plhak; David Bednar; Sérgio M. Marques; Jan Brezovsky; Jan Stourac; Ludek Matyska; Jirí Damborský (Bioinform., 2019)

Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. - Jan Byska; Thomas Trautner; Sérgio M. Marques; Jirí Damborský; Barbora Kozlíková; Manuela Waldner (Comput. Graph. Forum, 2019)

CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. - Jiri Filipovic; Ondrej Vávra; Jan Plhak; David Bednar; Sérgio M. Marques; Jan Brezovsky; Ludek Matyska; Jirí Damborský (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

sMolBoxes: Dataflow Model for Molecular Dynamics Exploration. - Pavol Ulbrich; Manuela Waldner; Katarína Furmanová; Sérgio M. Marques; David Bednár; Barbora Kozlíková; Jan Byska (IEEE Trans. Vis. Comput. Graph., 2023)

InVADo: Interactive Visual Analysis of Molecular Docking Data. - Marco Schäfer; Nicolas Brich; Jan Byska; Sérgio M. Marques; David Bednár; Philipp Thiel; Barbora Kozlíková; Michael Krone (IEEE Trans. Vis. Comput. Graph., 2024)

Decoding Protein Stabilization: Impact on Aggregation, Solubility, and Unfolding Mechanisms. - Martin Havlásek; Sérgio M. Marques; Veronika Szotkowska; Antonin Kunka; Petra Babková; Jirí Damborský; Zbynek Prokop; David Bednár (J. Chem. Inf. Model., 2025)

Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands. - Radek Halfar; Jirí Damborský; Sérgio M. Marques; Jan Martinovic (J. Cheminformatics, 2025)