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Protocols

OCHEM specifications

Information


Unique identifier OMICS_06438
Name OCHEM
Alternative name Online Chemical Modeling Environment
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Valery Tkachenko

Publications for Online Chemical Modeling Environment

OCHEM citations

 (15)
library_books

Comparing the performance of meta classifiers—a case study on selected imbalanced data sets relevant for prediction of liver toxicity

2018
J Comput Aided Mol Des
PMCID: 5919997
PMID: 29626291
DOI: 10.1007/s10822-018-0116-z

[…] y one way of stratified learning, i.e., under-sampling stratified bagging, was used in the study, we refer to it as “Stratified Bagging”.Bagging and Stratified Bagging were used as implemented in the Online Chemical Modeling Environment (OCHEM) [, ]. For other meta-classifiers, WEKA(v. 3-7-12) [, ] was used.Cost sensitive classifier [–, , ] is a meta-classifier that renders the base classifier cos […]

library_books

An automated framework for QSAR model building

2018
J Cheminform
PMCID: 5770354
PMID: 29340790
DOI: 10.1186/s13321-017-0256-5

[…] lows automated QSAR mainly by a command line interface. Python programming skills are necessary to work with eTOXlab. An interesting alternative of integrated solution for fully automated modeling is OCHEM [] but it’s online nature makes it unsuitable for using it with private/sensitive data sets, which demand better privacy and safety independent of third party. Cox et al. [] designed a Pipeline […]

call_split

Identification of potential antimicrobials against Salmonella typhimurium and Listeria monocytogenes using Quantitative Structure Activity Relation modeling

2017
PLoS One
PMCID: 5728541
PMID: 29236763
DOI: 10.1371/journal.pone.0189580
call_split See protocol

[…] The molecular descriptors for all data sets were calculated using the ochem.eu chemoinformatics database (https://ochem.eu). The “Calculate Descriptors” bar was accessed under the “Models” tab, and the Excel files were uploaded directly to the server. The uploaded molec […]

library_books

Matched Molecular Pair Analysis on Large Melting Point Datasets: A Big Data Perspective

2017
ChemMedChem
PMCID: 5900986
PMID: 28650584
DOI: 10.1002/cmdc.201700303

[…] Datasets: For this study, we used a dataset published by Tetko et al. The dataset is publicly available on OCHEM (Online Chemical Database with Modelling Environment), and contains 275 133 compounds covering a wide range of melting points, primarily in the drug‐like range (50–250 °C). These data were taken […]

library_books

A novel applicability domain technique for mapping predictive reliability across the chemical space of a QSAR: reliability density neighbourhood

2016
J Cheminform
PMCID: 5395519
DOI: 10.1186/s13321-016-0182-y

[…] (“CYP450 modulation e-state” model entry, referred to as “CYP450” from now on). To avoid any additional bias, the datasets were previously modelled [] and the predictions were used as provided at the OChem QSAR modelling repository (https://ochem.eu/home/show.do). To allow testing the robustness of the AD profile, the validation datasets retrieved from OChem were split into two. Therefore, in this […]

library_books

ToxCast EPA in Vitro to in Vivo Challenge: Insight into the Rank I Model

2016
Chem Res Toxicol
PMCID: 5413193
PMID: 27120770
DOI: 10.1021/acs.chemrestox.5b00481

[…] ge was a consensus of the bagging models developed with the ASNN method. In this section, we briefly describe the considerations that were used to develop and select this model for the challenge. The OCHEM Web site provides several machine learning methods and descriptors. Below, we compare the performance of different methods, which are described in the section.Bagging vs cross-validation was co […]

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