Peer-reviewed articles

  1. Hanson RM, Mayfield J, Vainio MJ, Yerin A, Redkin D, Musacchio S (2018) Algorithmic Analysis of Cahn-Ingold-Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation. J. Chem. Inf. Model. 58: 1755-1765.
  2. Vainio MJ, Kogej T, Raubacher F, Sadowski J (2013) Scaffold Hopping by Fragment Replacement. J. Chem. Inf. Model. 53: 1825-1835.
  3. Kogej T, Blomberg N, Greasley PJ, Mundt S, Vainio MJ, Schamberger J, Schmidt G, Hüser J (2013) Big pharma screening collections: more of the same or unique libraries? The AstraZeneca-Bayer Pharma AG case. Drug Discov. Today 18: 1014-1024.
  4. Vainio MJ, Kogej T, Raubacher F (2012) Automated Recycling of Chemistry for Virtual Screening and Library Design. J. Chem. Inf. Model. 52: 1777-1786.
  5. Gupta S, Fallarero A, Vainio MJ, P. Saravanan, Puranen JS, Järvinen P, Johnson MS, Vuorela RM, Mohan CG (2011) Molecular Docking Guided Comparative GFA, G/PLS, SVM and ANN Models of Structurally Diverse Dual Binding Site Acetylcholinesterase Inhibitors. Mol. Inf. 30: 689-706.
  6. Puranen JS, Vainio MJ, Johnson MS. (2010) Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery. J. Comput. Chem. 31: 1722-1732.
  7. Riihimaki-Lampen LH, Vainio MJ, Vahermo M, Pohjala LL, Heikura JM, Valkonen KH, Virtanen VT, Yli-Kauhaluoma JT, Vuorela PM. (2010) The Binding of Synthetic Retinoids to Lipocalin beta-Lactoglobulins. J. Med. Chem. 53: 514-518.
  8. Vainio MJ, Puranen JS, Johnson MS. (2009) ShaEP: molecular overlay based on shape and electrostatic potential. J. Chem. Inf. Model. 49: 492-502.
  9. Riihimaki LH, Vainio MJ, Heikura JM, Valkonen KH, Virtanen VT, Vuorela PM. (2008) Binding of phenolic compounds and their derivatives to bovine and reindeer beta-lactoglobulin. J. Agric. Food Chem. 56: 7721-7729.
  10. Vainio MJ, Johnson MS. (2007) Generating conformer ensembles using a multiobjective genetic algorithm. J. Chem. Inf. Model. 47: 2462-2474.
  11. Alvesalo JK, Siiskonen A, Vainio MJ, Tammela PS, Vuorela PM. (2006) Similarity based virtual screening: a tool for targeted library design. J. Med. Chem. 49: 2353-2356.
  12. Vainio MJ, Johnson MS. (2005) McQSAR: a multiconformational quantitative structure-activity relationship engine driven by genetic algorithms. J. Chem. Inf. Model. 45: 1953-1961.