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1. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

Author

Sushko I, Pandey AK, Novotarskyi S, Körner R, Rupp M, Teetz W, Brandmaier S, Abdelaziz A, Prokopenko VV, Tanchuk VY, Todeschini R, Varnek A, Marcou G, Ertl P, Potemkin V, Grishina M, Gasteiger J, Baskin II, Palyulin VA, Radchenko EV, Welsh WJ, Kholodovych V, Chekmarev D, Cherkasov A, Aires-de-Sousa J, Zhang Q-Y, Bender A, Nigsch F, Patiny L, Williams A, Tkachenko V, and Tetko IV

Subjects
Information technology, T58.5-58.64, Chemistry, QD1-999
Published
2011
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8. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

Author

Gilles Marcou, Florian Nigsch, Ahmed Abdelaziz, Qingyou Zhang, Vladyslav Kholodovych, William J. Welsh, Matthias Rupp, Antony J. Williams, Vsevolod Yu. Tanchuk, Valery Tkachenko, Volodymyr V. Prokopenko, Sergii Novotarskyi, Alexandre Varnek, Igor I. Baskin, Christof H. Schwab, Peter Ertl, João Aires-de-Sousa, Eugene V. Radchenko, Johann Gasteiger, Robert Körner, Igor V. Tetko, Iurii Sushko, Andreas Bender, Maria Grishina, Vladimir A. Palyulin, Dmitriy Chekmarev, Luc Patiny, Wolfram Teetz, Artem Cherkasov, Stefan Brandmaier, Roberto Todeschini, Anil Kumar Pandey, Vladimir Potemkin, Sushko, I, Novotarskyi, S, Körner, R, Pandey, A, Rupp, M, Teetz, W, Brandmaier, S, Abdelaziz, A, Prokopenko, V, Tanchuk, V, Todeschini, R, Varnek, A, Marcou, G, Ertl, P, Potemkin, V, Grishina, M, Gasteiger, J, Schwab, C, Baskin, I, Palyulin, V, Radchenko, E, Welsh, W, Kholodovych, V, Chekmarev, D, Cherkasov, A, Aires de Sousa, J, Zhang, Q, Bender, A, Nigsch, F, Patiny, L, and Williams, A

Subjects
Information management, Databases, Factual, Computer science, Estimation of accuracy of predictions, Information Management, Molecular Similarity, Modeling workflow, Quantitative Structure-Activity Relationship, 01 natural sciences, Partition-Coefficients, Descriptors, Article, Set (abstract data type), World Wide Web, 03 medical and health sciences, User-Computer Interface, Resource (project management), CHIM/01 - CHIMICA ANALITICA, Applicability domain, Drug Discovery, Physical and Theoretical Chemistry, 030304 developmental biology, 0303 health sciences, Internet, On-line web platform, business.industry, Information Dissemination, Open access, E-State Indexes, 0104 chemical sciences, Variety (cybernetics), Computer Science Applications, Data sharing, 010404 medicinal & biomolecular chemistry, On-line web platform, Modeling workflow, Estimation of accuracy of predictions, Applicability domain, Data sharing, Open access, In-Silico, Models, Chemical, Cheminformatics, Shape Signatures, Associative Neural Networks, The Internet, ddc:004, business, Prediction
Abstract

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 thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu . © 2011 The Author(s).

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9. CADASTER QSPR Models for Predictions of Melting and Boiling Points of Perfluorinated Chemicals.

Author

Bhhatarai B, Teetz W, Liu T, Öberg T, Jeliazkova N, Kochev N, Pukalov O, Tetko IV, Kovarich S, Papa E, and Gramatica P

Abstract

Quantitative structure property relationship (QSPR) studies on per- and polyfluorinated chemicals (PFCs) on melting point (MP) and boiling point (BP) are presented. The training and prediction chemicals used for developing and validating the models were selected from Syracuse PhysProp database and literatures. The available experimental data sets were split in two different ways: a) random selection on response value, and b) structural similarity verified by self-organizing-map (SOM), in order to propose reliable predictive models, developed only on the training sets and externally verified on the prediction sets. Individual linear and non-linear approaches based models developed by different CADASTER partners on 0D-2D Dragon descriptors, E-state descriptors and fragment based descriptors as well as consensus model and their predictions are presented. In addition, the predictive performance of the developed models was verified on a blind external validation set (EV-set) prepared using PERFORCE database on 15 MP and 25 BP data respectively. This database contains only long chain perfluoro-alkylated chemicals, particularly monitored by regulatory agencies like US-EPA and EU-REACH. QSPR models with internal and external validation on two different external prediction/validation sets and study of applicability-domain highlighting the robustness and high accuracy of the models are discussed. Finally, MPs for additional 303 PFCs and BPs for 271 PFCs were predicted for which experimental measurements are unknown., (Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Published
2011
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