McQSAR: A Multiconformational Quantitative Structure-Activity Relationship Engine Driven by Genetic Algorithms. - Mikko J. Vainio; Mark S. Johnson (J. Chem. Inf. Model., 2005)

Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm. - Mikko J. Vainio; Mark S. Johnson (J. Chem. Inf. Model., 2007)

ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential. - Mikko J. Vainio; J. Santeri Puranen; Mark S. Johnson (J. Chem. Inf. Model., 2009)

Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery. - J. Santeri Puranen; Mikko J. Vainio; Mark S. Johnson (J. Comput. Chem., 2010)

Automated Recycling of Chemistry for Virtual Screening and Library Design. - Mikko J. Vainio; Thierry Kogej; Florian Raubacher (J. Chem. Inf. Model., 2012)

Scaffold Hopping by Fragment Replacement. - Mikko J. Vainio; Thierry Kogej; Florian Raubacher; Jens Sadowski (J. Chem. Inf. Model., 2013)

Algorithmic Analysis of Cahn-Ingold-Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation. - Robert M. Hanson; Sophia Musacchio; John W. Mayfield; Mikko J. Vainio; Andrey Yerin; Dmitry Redkin (J. Chem. Inf. Model., 2018)