Volodymyr V. Prokopenko

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Internet technology offers an excellent opportunity for the development of tools by the cooperative effort of various groups and institutions. We have developed a multi-platform software system, Virtual Computational Chemistry Laboratory, http://www.vcclab.org, allowing the computational chemist to perform a comprehensive series of molecular(More)
The estimation of accuracy and applicability of QSAR and QSPR models for biological and physicochemical properties represents a critical problem. The developed parameter of "distance to model" (DM) is defined as a metric of similarity between the training and test set compounds that have been subjected to QSAR/QSPR modeling. In our previous work, we(More)
The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of(More)
A series of diverse organic compounds, phosphodiesterase type 4 (PDE-4) inhibitors, have been modeled using a QSAR-based approach. 48 QSAR models were compared by following the same procedure with different combinations of descriptors and machine learning methods. QSAR methodologies used random forests and associative neural networks. The predictive ability(More)
The Maximal Margin (MAMA) linear programming classification algorithm has recently been proposed and tested for cancer classification based on expression data. It demonstrated sound performance on publicly available expression datasets. We developed a web interface to allow potential users easy access to the MAMA classification tool. Basic and advanced(More)
The prioritisation of chemical compounds is important for the identification of those chemicals that represent the highest threat to the environment. As part of the CADASTER project (http: / /www.cadaster.eu), we developed an online web tool that allows the calculation of the environmental risk of chemical compounds from a web interface. The environmental(More)
The influence of physical and chemical properties of some sites of transmembrane receptor domains on the receptors ability to interact with nonspecific antagonists was investigated mathematically. The properties of sites located in 3rd and 7th transmembrane domains are most likely to explain pharmacological characteristics of the receptors. The possibility(More)
Using experimental transcription model in vitro, and method of electron-topological calculations the elements of pharmacological and structural community have been found in the groups of physiologically active compounds (PAC), blocking and activating external cellular receptors. This finding confirms the necessity of subdivision special groups of(More)
A substrate and inhibitor analysis of the thrombin interaction with synthetic peptide substrates and inhibitors of differing hydrophobicity and volume of the side amino acid residue, localized in the sub-centers thrombin S2 and S3 were carried out. The kinetic parameters of individual stages of the enzymatic reaction process (K(S), k2, k3) were estimated.(More)
The main goal of OCHEM database http://qspr.eu is to collect, store and manipulate chemical data with the purpose of their use for model development. Its main features, that distinguish it from other available databases include: 1. The database is open and it is based on Wiki-style principles. We encourage users to submit data and to correct inaccurate(More)