A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP): Theory and Application. - Massimo Baroni; Gabriele Cruciani; Simone Sciabola; Francesca Perruccio; Jonathan S. Mason (J. Chem. Inf. Model., 2007)

Pharmacophoric Fingerprint Method (TOPP) for 3D-QSAR Modeling: Application to CYP2D6 Metabolic Stability. - Simone Sciabola; Iñaki Morao; Marcel J. de Groot (J. Chem. Inf. Model., 2007)

Predicting Kinase Selectivity Profiles Using Free-Wilson QSAR Analysis. - Simone Sciabola; Robert V. Stanton; Sarah Wittkopp; Scott A. Wildman; Deborah J. Moshinsky; Shobha Potluri; Hualin Xi (J. Chem. Inf. Model., 2008)

High-Throughput Virtual Screening of Proteins Using GRID Molecular Interaction Fields. - Simone Sciabola; Robert V. Stanton; James E. J. Mills; Maria M. Flocco; Massimo Baroni; Gabriele Cruciani; Francesca Perruccio; Jonathan S. Mason (J. Chem. Inf. Model., 2010)

Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction. - Qin Wang 010; Simone Sciabola; Gabriela Barreiro; Xinjun Hou; Guoyun Bai; Michael J. Shapiro; Frank Koehn; Anabella Villalobos; Matthew P. Jacobson (J. Chem. Inf. Model., 2016)

A Transformer-based Generative Model for De Novo Molecular Design. - Wenlu Wang; Ye Wang 024; Honggang Zhao; Simone Sciabola (CoRR, 2022)

Large-scale Pretraining Improves Sample Efficiency of Active Learning based Molecule Virtual Screening. - Zhonglin Cao; Simone Sciabola; Ye Wang 024 (CoRR, 2023)

Prospective Validation of Machine Learning Algorithms for Absorption, Distribution, Metabolism, and Excretion Prediction: An Industrial Perspective. - Cheng Fang; Ye Wang 024; Richard Grater; Sudarshan Kapadnis; Cheryl Black; Patrick E. Trapa; Simone Sciabola (J. Chem. Inf. Model., 2023)

ROSHAMBO: Open-Source Molecular Alignment and 3D Similarity Scoring. - Rasha Atwi; Ye Wang 024; Simone Sciabola; Adam Antoszewski (J. Chem. Inf. Model., 2024)

ACEGEN: Reinforcement Learning of Generative Chemical Agents for Drug Discovery. - Albert Bou; Morgan Thomas; Sebastian Dittert; Carles Navarro; Maciej Majewski; Ye Wang 024; Shivam Patel; Gary Tresadern; Mazen Ahmad; Vincent Moens; Woody Sherman; Simone Sciabola; et al. (J. Chem. Inf. Model., 2024)

Large-Scale Pretraining Improves Sample Efficiency of Active Learning-Based Virtual Screening. - Zhonglin Cao; Simone Sciabola; Ye Wang 024 (J. Chem. Inf. Model., 2024)