BODIL: a molecular modeling environment for structure-function analysis and drug design. - Jukka V. Lehtonen; Dan-Johan Still; Ville-Veikko Rantanen; Jan Ekholm; Dag Björklund; Zuhair Iftikhar; Mikko Huhtala; Susanna Repo; Antti Jussila; Jussi Jaakkola; Olli T. Pentikäinen; Tommi H. Nyrönen; et al. (J. Comput. Aided Mol. Des., 2004)

Efficient Virtual Screening Using Multiple Protein Conformations Described as Negative Images of the Ligand-Binding Site. - Salla I. Virtanen; Olli T. Pentikäinen (J. Chem. Inf. Model., 2010)

Comparison of Virtual High-Throughput Screening Methods for the Identification of Phosphodiesterase-5 Inhibitors. - Sanna P. Niinivehmas; Salla I. Virtanen; Jukka V. Lehtonen; Pekka A. Postila; Olli T. Pentikäinen (J. Chem. Inf. Model., 2011)

Full and Partial Agonism of Ionotropic Glutamate Receptors Indicated by Molecular Dynamics Simulations. - Pekka A. Postila; Mikko Ylilauri; Olli T. Pentikäinen (J. Chem. Inf. Model., 2011)

MMGBSA As a Tool To Understand the Binding Affinities of Filamin-Peptide Interactions. - Mikko Ylilauri; Olli T. Pentikäinen (J. Chem. Inf. Model., 2013)

Ultrafast protein structure-based virtual screening with Panther. - Sanna P. Niinivehmas; Kari Salokas; Sakari Lätti; Hannu Raunio; Olli T. Pentikäinen (J. Comput. Aided Mol. Des., 2015)

Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization. - Sakari Lätti; Sanna P. Niinivehmas; Olli T. Pentikäinen (J. Cheminformatics, 2016)

Getting Docking into Shape Using Negative Image-Based Rescoring. - Sami T. Kurkinen; Sakari Lätti; Olli T. Pentikäinen; Pekka A. Postila (J. Chem. Inf. Model., 2019)

Detection of Binding Sites on SARS-CoV-2 Spike Protein Receptor-Binding Domain by Molecular Dynamics Simulations in Mixed Solvents. - Elmeri M. Jokinen; Krishnasamy Gopinath; Sami T. Kurkinen; Olli T. Pentikäinen (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Optimization of Cavity-Based Negative Images to Boost Docking Enrichment in Virtual Screening. - Sami T. Kurkinen; Jukka V. Lehtonen; Olli T. Pentikäinen; Pekka A. Postila (J. Chem. Inf. Model., 2022)

Sdfconf: A Novel, Flexible, and Robust Molecular Data Management Tool. - Sakari Lätti; Sanna P. Niinivehmas; Olli T. Pentikäinen (J. Chem. Inf. Model., 2022)

Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1. - Aliaa E. Ali; Li-Li Li; Michael J. Courtney; Olli T. Pentikäinen; Pekka A. Postila (Briefings Bioinform., 2024)

Building shape-focused pharmacophore models for effective docking screening. - Paola Moyano-Gómez; Jukka V. Lehtonen; Olli T. Pentikäinen; Pekka A. Postila (J. Cheminformatics, 2024)