CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. - Pin-Chia Hsu; Bart M. H. Bruininks; Damien Jefferies; Paulo C. T. Souza; Jumin Lee; Dhilon S. Patel; Siewert J. Marrink; Yifei Qi; Syma Khalid; Wonpil Im (J. Comput. Chem., 2017)

High performance collision cross section calculation - HPCCS. - Leandro Zanotto; Gabriel Heerdt; Paulo C. T. Souza; Guido Araujo; Munir S. Skaf (J. Comput. Chem., 2018)

Martinize2 and Vermouth: Unified Framework for Topology Generation. - Peter C. Kroon; Fabian Grünewald; Jonathan Barnoud; Marco van Tilburg; Paulo C. T. Souza; Tsjerk A. Wassenaar; Siewert-Jan Marrink (CoRR, 2022)

Facilitating CG Simulations with MAD: The MArtini Database Server. - Cécile Hilpert; Louis Beranger; Paulo C. T. Souza; Petteri A. Vainikka; Vincent Nieto; Siewert J. Marrink; Luca Monticelli; Guillaume Launay (J. Chem. Inf. Model., 2023)

Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG. - Charly Empereur-mot; Kasper B. Pedersen; Riccardo Capelli; Martina Crippa; Cristina Caruso; Mattia Perrone; Paulo C. T. Souza; Siewert J. Marrink; Giovanni M. Pavan (J. Chem. Inf. Model., 2023)

Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking. - Gilberto Pereira; Brian Jiménez-García; Riccardo Pellarin; Guillaume Launay; Sangwook Wu; Juliette Martin; Paulo C. T. Souza (J. Chem. Inf. Model., 2023)

Creating Coarse-Grained Systems with COBY: Toward Higher Accuracy of Complex Biological Systems. - Mikkel D. Andreasen; Paulo C. T. Souza; Birgit Schiøtt; Lorena Zuzic (J. Chem. Inf. Model., 2025)

Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field. - Astrid F. Brandner; Iain Peter Shand Smith; Siewert J. Marrink; Paulo C. T. Souza; Syma Khalid (J. Chem. Inf. Model., 2025)