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

被引：492

作者：

Sushko, Iurii ^{[1
,2
]}

Novotarskyi, Sergii ^{[1
,2
]}

Koerner, Robert ^{[1
,2
]}

Pandey, Anil Kumar ^{[2
]}

Rupp, Matthias ^{[2
]}

Teetz, Wolfram ^{[1
,2
]}

Brandmaier, Stefan ^{[2
]}

Abdelaziz, Ahmed ^{[1
,2
]}

Prokopenko, Volodymyr V. ^{[3
]}

Tanchuk, Vsevolod Y. ^{[3
]}

Todeschini, Roberto ^{[4
]}

Varnek, Alexandre ^{[5
]}

Marcou, Gilles ^{[5
]}

Ertl, Peter ^{[6
]}

Potemkin, Vladimir ^{[7
]}

Grishina, Maria ^{[7
]}

Gasteiger, Johann ^{[8
]}

Schwab, Christof ^{[8
]}

Baskin, Igor I. ^{[9
]}

Palyulin, Vladimir A. ^{[9
]}

Radchenko, Eugene V. ^{[9
]}

Welsh, William J. ^{[10
,11
]}

Kholodovych, Vladyslav ^{[10
,11
]}

Chekmarev, Dmitriy ^{[10
,11
]}

Cherkasov, Artem ^{[12
]}

Aires-de-Sousa, Joao ^{[13
]}

Zhang, Qing-You ^{[14
]}

Bender, Andreas ^{[15
]}

Nigsch, Florian ^{[16
]}

Patiny, Luc ^{[17
]}

Williams, Antony ^{[18
]}

Tkachenko, Valery ^{[18
]}

Tetko, Igor V. ^{[1
,2
]}

机构：

[1] eADMET GmbH, D-85764 Neuherberg, Germany

[2] German Res Ctr Environm Hlth GmbH, Helmholtz Zentrum Munchen, D-85764 Neuherberg, Germany

[3] Inst Bioorgan & Petrochem, UA-253660 Kiev, Ukraine

[4] Univ Milano Bicocca, Milano Chemometr & QSAR Res Grp, Dept Environm Sci, I-20126 Milan, Italy

[5] Univ Strasbourg, Lab Infochim, CNRS, UMR 7177, F-67000 Strasbourg, France

[6] Novartis Inst BioMed Res, CH-4056 Basel, Switzerland

[7] Chelyabinsk State Med Acad, Chelyabinsk, Russia

[8] Mol Networks GmbH, D-91052 Erlangen, Germany

[9] Moscow MV Lomonosov State Univ, Dept Chem, Moscow 119991, Russia

[10] UMDNJ, Robert Wood Johnson Med Sch, Dept Pharmacol, Piscataway, NJ 08854 USA

[11] UMDNJ, Robert Wood Johnson Med Sch, ebCTC, Piscataway, NJ 08854 USA

[12] Univ British Columbia, Vancouver Prostate Ctr, Fac Med, Vancouver, BC V6H 3Z6, Canada

[13] Univ Nova Lisboa, CQFB, REQUIMTE, Dept Quim,Fac Ciencias & Tecnol, P-2829516 Caparica, Portugal

[14] Henan Univ, Inst Environm & Analyt Sci, Coll Chem & Chem Engn, Kaifeng 475004, Peoples R China

[15] Univ Cambridge, Unilever Ctr Mol Sci Informat, Cambridge CB2 1EW, England

[16] Novartis Inst BioMed Res Inc, Cambridge, MA 02139 USA

[17] Ecole Polytech Fed Lausanne, CH-1015 Lausanne, Switzerland

[18] Royal Soc Chem, Wake Forest, NC 27587 USA

来源：

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN | 2011年 / 25卷 / 06期

关键词：

On-line web platform; Modeling workflow; Estimation of accuracy of predictions; Applicability domain; Data sharing; Open access; ASSOCIATIVE NEURAL NETWORKS; E-STATE INDEXES; SHAPE SIGNATURES; IN-SILICO; MOLECULAR SIMILARITY; DRUG DISCOVERY; PARTITION-COEFFICIENTS; APPLICABILITY DOMAIN; PREDICTION; DESCRIPTORS;

D O I：

10.1007/s10822-011-9440-2

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：533 / 554

页数：22

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