Peer-reviewed articles
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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.
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Vainio MJ, Kogej T, Raubacher F, Sadowski J (2013)
Scaffold Hopping by Fragment Replacement.
J. Chem. Inf. Model. 53: 1825-1835.
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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.
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Vainio MJ, Kogej T, Raubacher F (2012)
Automated Recycling of Chemistry for Virtual Screening and Library Design.
J. Chem. Inf. Model. 52: 1777-1786.
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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.
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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.
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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.
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Vainio MJ, Puranen JS, Johnson MS.
(2009)
ShaEP: molecular overlay based on shape and electrostatic potential.
J. Chem. Inf. Model. 49: 492-502.
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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.
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Vainio MJ, Johnson MS.
(2007)
Generating conformer ensembles using a multiobjective genetic algorithm.
J. Chem. Inf. Model. 47: 2462-2474.
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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.
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Vainio MJ, Johnson MS.
(2005)
McQSAR: a multiconformational quantitative structure-activity relationship engine driven by genetic algorithms.
J. Chem. Inf. Model. 45: 1953-1961.