The Human Genome and High Performance Computing in Molecular Biology. - Chris Sander; Reinhard Schneider 002; Pieter F. W. Stouten (Supercomputer, 1992)

A Molecular Mechanics/Grid Method for Evaluation of Ligand-Receptor Interactions. - Brock A. Luty; Zelda R. Wasserman; Pieter F. W. Stouten; C. Nicholas Hodge; Martin Zacharias; James Andrew McCammon (J. Comput. Chem., 1995)

Fast prediction and visualization of protein binding pockets with PASS. - G. Patrick Brady Jr.; Pieter F. W. Stouten (J. Comput. Aided Mol. Des., 2000)

Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculations. - Lu Wang; Yong Duan; Pieter F. W. Stouten; George V. De Lucca; Ronald M. Klabe; Peter A. Kollman (J. Comput. Aided Mol. Des., 2001)

Novel Scoring Functions Comprising QXP, SASA, and Protein Side-Chain Entropy Terms. - Fabrizio Giordanetto; Simona Cotesta; Cornel Catana; Jean-Yves Trosset; Anna Vulpetti; Pieter F. W. Stouten; Romano T. Kroemer (J. Chem. Inf. Model., 2004)

Assessment of Docking Poses: Interactions-Based Accuracy Classification (IBAC) versus Crystal Structure Deviations. - Romano T. Kroemer; Anna Vulpetti; Joseph J. McDonald; Douglas C. Rohrer; Jean-Yves Trosset; Fabrizio Giordanetto; Simona Cotesta; Colin McMartin; Mats Kihlén; Pieter F. W. Stouten (J. Chem. Inf. Model., 2004)

Understanding and modulating cyclin-dependent kinase inhibitor specificity: molecular modeling and biochemical evaluation of pyrazolopyrimidinones as CDK2/cyclin A and CDK4/cyclin D1 inhibitors. - Karen A. Rossi; Jay A. Markwalder; Steven P. Seitz; Chong-Hwan Chang; Sarah Cox; Michael D. Boisclair; Leonardo Brizuela; Stephen L. Brenner; Pieter F. W. Stouten (J. Comput. Aided Mol. Des., 2005)

Linear and Nonlinear Methods in Modeling the Aqueous Solubility of Organic Compounds. - Cornel Catana; Hua Gao; Christian Orrenius; Pieter F. W. Stouten (J. Chem. Inf. Model., 2005)

Novel, Customizable Scoring Functions, Parameterized Using N-PLS, for Structure-Based Drug Discovery. - Cornel Catana; Pieter F. W. Stouten (J. Chem. Inf. Model., 2007)

Shedding Light on Important Waters for Drug Design: Simulations versus Grid-Based Methods. - Denis Bucher; Pieter F. W. Stouten; Nicolas Triballeau (J. Chem. Inf. Model., 2018)

Multitask machine learning models for predicting lipophilicity (logP) in the SAMPL7 challenge. - Eelke B. Lenselink; Pieter F. W. Stouten (J. Comput. Aided Mol. Des., 2021)

Large-Scale Modeling of Sparse Protein Kinase Activity Data. - Sohvi Luukkonen; Erik Meijer 004; Giovanni Tricarico; Johan Hofmans; Pieter F. W. Stouten; Gerard J. P. van Westen; Eelke B. Lenselink (J. Chem. Inf. Model., 2023)

"DompeKeys": a set of novel substructure-based descriptors for efficient chemical space mapping, development and structural interpretation of machine learning models, and indexing of large databases. - Candida Manelfi; Valerio Tazzari; Filippo Lunghini; Carmen Cerchia; Anna Fava; Alessandro Pedretti; Pieter F. W. Stouten; Giulio Vistoli; Andrea Rosario Beccari (J. Cheminformatics, 2024)