BUNDLE: A program for building the transmembrane domains of G-protein-coupled receptors. - Marta Filizola; Juan Jesús Pérez; Maria Cartenì-Farina (J. Comput. Aided Mol. Des., 1998)

Molecular modeling study of the differential ligand-receptor interaction at the µ, delta and kappa opioid receptors. - Marta Filizola; Maria Cartenì-Farina; Juan Jesús Pérez (J. Comput. Aided Mol. Des., 1999)

Differentiation of delta, µ, and kappa opioid receptor agonists based on pharmacophore development and computed physicochemical properties. - Marta Filizola; Hugo O. Villar; Gilda H. Loew (J. Comput. Aided Mol. Des., 2001)

Global physicochemical properties as activity discriminants for the mGluR1 subtype of metabotropic glutamate receptors. - Marta Filizola; Silvina M. Tasso; Gilda H. Loew; Hugo O. Villar (J. Comput. Chem., 2001)

Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer. - Marta Filizola; Simon X. Wang; Harel Weinstein (J. Comput. Aided Mol. Des., 2006)

TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations. - Mihaly Mezei; Marta Filizola (J. Comput. Aided Mol. Des., 2006)

Modeling activated states of GPCRs: the rhodopsin template. - Masha Y. Niv; Lucy Skrabanek; Marta Filizola; Harel Weinstein (J. Comput. Aided Mol. Des., 2006)

Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base. - Lucy Skrabanek; Marta Murcia; Michel Bouvier; Lakshmi Devi; Susan R. George; Martin J. Lohse; Graeme Milligan; Richard R. Neubig; Krzysztof Palczewski; Marc Parmentier; Jean-Philippe Pin; Gerrit Vriend; et al. (BMC Bioinform., 2007)

GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base. - George Khelashvili; Kevin C. Dorff; Jufang Shan; Marta Camacho-Artacho; Lucy Skrabanek; Bas Vroling; Michel Bouvier; Lakshmi Devi; Susan R. George; Jonathan A. Javitch; Martin J. Lohse; Graeme Milligan; et al. (Bioinform., 2010)

Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques. - Davide Provasi; Marta Camacho-Artacho; Ana Negri; Juan Carlos Mobarec; Marta Filizola (PLoS Comput. Biol., 2011)

Structure-based virtual screening of small-molecule antagonists of platelet integrin αIIbβ3 that do not prime the receptor to bind ligand. - Ana Negri; Jihong Li; Sarasija Naini; Barry S. Coller; Marta Filizola (J. Comput. Aided Mol. Des., 2012)

Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors. - Jennifer M. Johnston; Hao Wang; Davide Provasi; Marta Filizola (PLoS Comput. Biol., 2012)

Discovery of a Novel Selective Kappa-Opioid Receptor Agonist Using Crystal Structure-Based Virtual Screening. - Ana Negri; Marie-Laure Rives; Michael J. Caspers; Thomas E. Prisinzano; Jonathan A. Javitch; Marta Filizola (J. Chem. Inf. Model., 2013)

Ligand-Based Discovery of a New Scaffold for Allosteric Modulation of the μ-Opioid Receptor. - Paola Bisignano; Neil T. Burford; Yi Shang; Brennica Marlow; Kathryn E. Livingston; Abigail M. Fenton; Kristin Rockwell; Lauren Budenholzer; John R. Traynor; Samuel W. Gerritz; Andrew Alt; Marta Filizola (J. Chem. Inf. Model., 2015)

Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association. - Davide Provasi; Mustafa Burak Boz; Jennifer M. Johnston; Marta Filizola (PLoS Comput. Biol., 2015)

Impact of Lipid Composition and Receptor Conformation on the Spatio-temporal Organization of μ-Opioid Receptors in a Multi-component Plasma Membrane Model. - Kristen A. Marino; Diego Prada-Gracia; Davide Provasi; Marta Filizola (PLoS Comput. Biol., 2016)

Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis. - Xiaohu Hu; Yibo Wang 011; Amanda Hunkele; Davide Provasi; Gavril W. Pasternak; Marta Filizola (PLoS Comput. Biol., 2019)

Structure-Based Discovery of a Novel Class of Small-Molecule Pure Antagonists of Integrin αVβ3. - Soumyo Sen; Aleksandar Spasic; Anjana Sinha; Jialing Wang; Martin Bush; Jihong Li; Dragana Nesic; Yuchen Zhou; Gabriella Angiulli; Paul Morgan; Leslie Salas-Estrada; Junichi Takagi; et al. (J. Chem. Inf. Model., 2022)

De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework. - Leslie Salas-Estrada; Davide Provasi; Xing Qiu; Husnu Ümit Kaniskan; Xi-Ping Huang; Jeffrey F. Diberto; João Marcelo Lamim Ribeiro; Jian Jin; Bryan L. Roth; Marta Filizola (J. Chem. Inf. Model., 2023)