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

Sushko, Iurii ; Novotarskyi, Sergii ; Korner, Robert ; Pandey, Anil Kumar ; Rupp, Matthias ; Teetz, Wolfram ; Brandmaier, Stefan ; Abdelaziz, Ahmed ; Prokopenko, Volodymyr V. ; Tanchuk, Vsevolod Y. ; Todeschini, Roberto ; Varnek, Alexandre ; Marcou, Gilles ; Ertl, Peter ; Potemkin, Vladimir ; Grishina, Maria ; Gasteiger, Johann ; Schwab, Christof ; Baskin, Igor I. ; Palyulin, Vladimir A. ; Radchenko, Eugene V. ; Welsh, William J. ; Kholodovych, Vladyslav ; Chekmarev, Dmitriy ; Cherkasov, Artem ; Aires - De - Sousa, Joao ; Zhang, Qing - You ; Bender, Andreas ; Nigsch, Florian ; Patiny, Luc ; Williams, Antony ; Tkachenko, Valery ; Tetko, Igor V.

Journal of Computer-Aided Molecular Design, June, 2011, Vol.25(6), p.533(22) [Peer Reviewed Journal]

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  • Title:
    Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information.(Report)
  • Author: Sushko, Iurii ; Novotarskyi, Sergii ; Korner, Robert ; Pandey, Anil Kumar ; Rupp, Matthias ; Teetz, Wolfram ; Brandmaier, Stefan ; Abdelaziz, Ahmed ; Prokopenko, Volodymyr V. ; Tanchuk, Vsevolod Y. ; Todeschini, Roberto ; Varnek, Alexandre ; Marcou, Gilles ; Ertl, Peter ; Potemkin, Vladimir ; Grishina, Maria ; Gasteiger, Johann ; Schwab, Christof ; Baskin, Igor I. ; Palyulin, Vladimir A. ; Radchenko, Eugene V. ; Welsh, William J. ; Kholodovych, Vladyslav ; Chekmarev, Dmitriy ; Cherkasov, Artem ; Aires - De - Sousa, Joao ; Zhang, Qing - You ; Bender, Andreas ; Nigsch, Florian ; Patiny, Luc ; Williams, Antony ; Tkachenko, Valery ; Tetko, Igor V.
  • Subjects: Medical Schools ; Information Storage And Retrieval ; Automation ; Computer Storage Devices ; Publishing Industry ; Environmental Health ; Internet Software ; Workflow Software
  • Is Part Of: Journal of Computer-Aided Molecular Design, June, 2011, Vol.25(6), p.533(22)
  • Description: Byline: Iurii Sushko (1,2), Sergii Novotarskyi (1,2), Robert Korner (1,2), Anil Kumar Pandey (2), Matthias Rupp (2), Wolfram Teetz (1,2), Stefan Brandmaier (2), Ahmed Abdelaziz (1,2), Volodymyr V. Prokopenko (3), Vsevolod Y. Tanchuk (3), Roberto Todeschini (4), Alexandre Varnek (5), Gilles Marcou (5), Peter Ertl (6), Vladimir Potemkin (7), Maria Grishina (7), Johann Gasteiger (8), Christof Schwab (8), Igor I. Baskin (9), Vladimir A. Palyulin (9), Eugene V. Radchenko (9), William J. Welsh (10), Vladyslav Kholodovych (10), Dmitriy Chekmarev (10), Artem Cherkasov (11), Joao Aires-de-Sousa (12), Qing-You Zhang (13), Andreas Bender (14), Florian Nigsch (15), Luc Patiny (16), Antony Williams (17), Valery Tkachenko (17), Igor V. Tetko (1,2) Keywords: On-line web platform; Modeling workflow; Estimation of accuracy of predictions; Applicability domain; Data sharing; Open access 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 . Author Affiliation: (1) eADMET GmbH, Ingolstadter Landstrasse 1, 85764, Neuherberg, Germany (2) Helmholtz Zentrum Munchen, German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, 85764, Neuherberg, Germany (3) Institute of Bioorganic & Petrochemistry, Murmanskaya 1, 253660, Kiev, Ukraine (4) Milano Chemometrics & QSAR Research Group, Department of Environmental Sciences, University of Milano-Bicocca, P.za della Scienza 1, 20126, Milan, Italy (5) Laboratoire d'Infochimie, UMR 7177 CNRS, Universite de Strasbourg, 4, rue B. Pascal, 67000, Strasbourg, France (6) Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland (7) Chelyabinsk State Medical Academy, Chelyabinsk, Russia (8) Molecular Networks GmbH, Henkestrasse 91, 91052, Erlangen, Germany (9) Department of Chemistry, Moscow State University, 119991, Moscow, Russia (10) Department of Pharmacology and Environmental Bioinformatics and Computational Toxicology Center (ebCTC), University of Medicine and Dentistry of New Jersey (UMDNJ)-Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA (11) Vancouver Prostate Centre, Faculty of Medicine, University of British Columbia, Vancouver, BC, V6H 3Z6, Canada (12) CQFB, REQUIMTE, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal (13) Institute of Environmental and Analytical Sciences, College of Chemistry and Chemical Engineering, Henan University, 475004, Kaifeng, China (14) Unilever Centre for Molecular Science Informatics, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK (15) Novartis Institutes for BioMedical Research, Inc., 250 Massachusetts Avenue, Cambridge, MA, 02139, USA (16) Ecole Polytechnique Federale de Lausanne, 1015, Lausanne, CH, Switzerland (17) Royal Society of Chemistry, 904 Tamaras Circle, Wake Forest, NC, 27587, USA Article History: Registration Date: 24/05/2011 Received Date: 22/02/2011 Accepted Date: 24/05/2011 Online Date: 10/06/2011 Article note: Iurii Sushko, Sergii Novotarskyi, Robert Korner and Anil Kumar Pandey made equal contributions to the article.
  • Language: English
  • Identifier: ISSN: 0920-654X

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