Scientific Publications

The following articles provide details on our SOM and virtual screening methods as well as how methods have been used for data clustering and visualization, and for virtual screening in different scientific fields. If you would like to know more about how Visipoint products have been utilized in a specific application, please contact us for additional details.

Index

• SOM Methods
• Virtual Screening Methods
• Biochemistry
• Environment
• Medicine
• Pharmaceutical Chemistry
• Pharmaceutical Technology
• Other

SOM Methods

Design, Implementation and Evaluation of Neural Data Analysis Environment. Häkkinen E, Jyväskylä Studies in Computing 12, University of Jyväskylä, 2001, Ph.D. Thesis.

Progress with the tree-structured self-organizing map. Koikkalainen P, Proceedings of ECAI´4, 11th European Conference on Artificial Intelligence (Cohn, A. G., Ed.), Wiley and Sons, New York. 1994, pp. 211-215

Virtual Screening Methods

Brutus - A Molecular Energy Field Based Superposition Algorithm for Virtual Screening. Rönkkö TP, Kuopio University Publications A. Pharmaceutical Sciences 188, 2009, Ph.D. Thesis.

ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential. Vainio M, Puranen S, Johnson M, J. Chem. Inf. Model., 49, 2009, pp. 492-502.

Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm. Vainio M, Johnson M, J. Chem. Inf. Model., 47, 2007, pp. 2462-2474.

BRUTUS: Optimization of a grid-based similarity function for rigid-body molecular superposition. II. Description and characterization. Rönkkö T, Tervo A, Parkkinen J, Poso A, J. Comput. Aided. Mol. Des., 20, 2006, pp. 227-236.

BRUTUS: Optimization of a grid-based similarity function for rigid-body molecular superposition. 1. alignment and virtual screening applications. Tervo A, Rönkkö T, Nyrönen T, Poso A, J. Med. Chem., 48, 2005, pp. 4076-4086.

Biochemistry

Vitamin D Receptor Agonists Specifically Modulate the Volume of the Ligand-binding Pocket. Molnár F, Peräkylä M, Carlberg C, J. Biol. Chem., 281, 2006, pp. 10516-10526.

Monitoring of yeast fermentation by ion Mobility spectrometry measurement and data visualisation with Self-organizing maps. Kolehmainen M, Rönkkö P, Raatikainen O, Anal. Chim. Acta, 484, 2003, pp. 93-100.

Analysis of gene expression data using self-organizing maps. Törönen P, Kolehmainen M, Wong G, Castren E, FEBS Lett., 451, 1999, pp. 142-146.

Methods of computational intelligence in handling ion mobility based IMCELL-measurement data from fermentation process. Kolehmainen M, University of Kuopio, 1997, M.Sc. Thesis.

Environment

Classification of Soil Groups Using Weights-of-Evidence-Method and RBFLN-Neural Nets. Tissari S, Nykänen V, Lerssi J, Kolehmainen M, Natural Resources Research, 16, 2007, pp. 159-169.

Neural networks and periodic components used in air quality forecasting. Kolehmainen M, Martikainen H, Ruuskanen J, Atmos. Environ., 35, 2001, pp. 815-825.

Determination and identification of pesticides from liquid matrices using ion mobility spectrometry. Tuovinen K, Kolehmainen M, Paakkanen H, Anal. Chim. Acta, 429, 2001, pp. 257-268.

Monitoring odorous sulfur emissions using Self-Organizing Maps for handling ion mobility spectrometry data. Kolehmainen M, Ruuskanen J, Rissanen E, Raatikainen O, J. Air & Waste Manage. Assoc., 51, 2001, pp. 966-971.

Forecasting air quality parameters using hybrid neural network modelling. Kolehmainen M, Martikainen H, Hiltunen T, Ruuskanen J, Environ. Monit. Assess., 65, 2000, pp. 277-286.

Medicine

Brain-derived neurotrophic factor signaling modifies hippocampal gene expression during epileptogenesis in transgenic mice. Lähteinen S, Pitkänen A, Knuuttila J, Törönen P, Castrén E, Eur. J. Neurosci., 19, 2004, pp. 3245-3254.

Insulin resistance syndrome revisited: application of Self-organizing maps, Valkonen V-P, Kolehmainen M, Lakka H-M, Salonen J, Int. J. Epidemiol., 31, 2002, pp. 864-871.

Antipsychotic drug treatment induces differential gene expression in the rat cortex. Kontkanen O, Törönen P, Lakso M, Wong G, Castrén E, J. Neurochem., 83, 2002, pp. 1043-1053.

Pharmaceutical Chemistry

Insights into Ligand-Elicited Activation of Human Constitutive Androstane Receptor Based on Novel Agonists and Three-Dimensional Quantitative Sructure-Activity Relationships. Jyrkkärinne J, Windshügel B, Rökkö T, Tervo A, Küblbeck J, Lahtela-Kakkonen M, Sippl W, Poso A, Honkakoski P, J. Med. Chem., 51, 2008, pp. 7181-7192

Fatty Acid Amide Hydrolase Inhibitors from Virtual Screening of the Endocannabinoid System. Saario S, Poso A, Juvonen R, Järvinen T, Salo-Ahen O, J. Med. Chem., 49, 2006, pp. 4650-4656.

Pharmaceutical Technology

Estimation of drug release profiles of a heterogeneous set of drugs from a hydrophobic matrix tablet using molecular descriptors. Matero S, Reinikainen S-P, Lahtela-Kakkonen M, Korhonen O, Ketolainen J, Poso A, J. Chemometrics, 22, 2008, pp. 653-660.

Chemical space of orally active compounds. Matero S, Lahtela-Kakkonen M, Korhonen O, Ketolainen J, Lappalainen R, Poso A, Chemom. Intell. Lab. Syst., 84, 2006, pp. 134-141.

Other

Comparison of structure fingerprint and molecular interaction field based methods in explaining biological similarity of small molecules in cell-based screens. Tiikkainen P, Poso A, Kallioniemi O, J. Comput. Aided Mol. Des., 23, 2009, pp. 227-239.

Data exploration with self-organizing maps in environmental informatics and bioinformatics. Kolehmainen M, University of Kuopio, 2004, Ph.D. Thesis.