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MassBank is the first public repository of mass spectra of small chemical compounds for life sciences (<3000 Da). The database contains 605 electron-ionization mass spectrometry (EI-MS), 137 fast atom bombardment MS and 9276 electrospray ionization (ESI)-MS(n) data of 2337 authentic compounds of metabolites, 11 545 EI-MS and 834 other-MS data of 10,286(More)
A spherical self-organizing map (SSOM) was applied for mapping the molecular surface of a protein structure on a spherical structure. The active site of the X-ray crystal structure of β2 receptor protein was used for this purpose. After mapping the molecular surface points and assigning the associated molecular electrostatic potential (MEP) values, the(More)
Comparative molecular field analysis (CoMFA) with partial least squares (PLS) is one of the most frequently used tools in three-dimensional quantitative structure-activity relationships (3D-QSAR) studies. Although many successful CoMFA applications have proved the value of this approach, there are some problems in its proper application. Especially, the(More)
The GAPLS (GA based PLS) program has been developed for variable selection in QSAR studies. The modified GA was employed to obtain a PLS model with high internal predictivity using a small number of variables. In order to show the performance of GAPLS for variable selection, the program was applied to the inhibitor activity of calcium channel antagonists.(More)
Comparative molecular field analysis (CoMFA) has been widely used as a standard three dimensional quantitative structure-activity relationship (3D-QSAR) method. Although CoMFA is a useful technique, it does not always reflect real ligand-receptor interaction. Molecular interactions between the ligand and receptor are mainly occurred near the van der Waals(More)
In quantitative structure-activity relationship (QSAR), multivariate statistical methods are commonly used for data analysis. Partial least squares (PLS) is of particular interest because it can analyze data with strongly collinear, noisy and numerous X variables, and also simultaneously models several activity variables Y. PLS provides several prediction(More)
Recently, we investigated and proposed the novel molecular alignment method with the Hopfield Neural Network (HNN). Molecules are represented by four kinds of chemical properties (hydrophobic group, hydrogen-bonding acceptor, hydrogen-bonding donor, and hydrogen-bonding donor/acceptor), and then those properties between two molecules correspond to each(More)
Quantitative structure-activity relationship (QSAR) studies based on chemometric techniques are reviewed. Partial least squares (PLS) is introduced as a novel robust method to replace classical methods such as multiple linear regression (MLR). Advantages of PLS compared to MLR are illustrated with typical applications. Genetic algorithm (GA) is a novel(More)