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Chemistry, Structural Alert, and QSAR Databases and Tools

  • PubChem63 provides information on the biological activities of small molecules. pubChem is organized as three linked databases within the national Center for Biotechnology Information’s Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool.
  • ChemSpider64 ChemSpider is a free chemical structure database providing fast text and structure search access to over 50 million structures from hundreds of data sources.
  • ChemProp65 Several modules including structural alerts for electrophilic reactivity.
  • • CORAL66Quantitative structure-property relationships (QSPR)/quantita- tive structure-activity relationships (QSAR) analysis for several toxicity endpoints.
  • OECD Toolbox67 QSAR toolbox for grouping chemicals into categories.
  • TEST63 The Toxicity Estimation Software Tool allows users to easily estimate the toxicity of chemicals using QSAR methodologies.
  • Virtual Computational Chemistry Laboratory69 On-line cheminformatics tools to calculate chemical properties including A Log P.
  • Danish (Q)SAR Database70 This Danish (Q)SAR database is a repository of estimates from over 70 (Q)SAR models for 166 072 chemicals. The (Q) SAR models encompass endpoints for physicochemical properties, fate, eco-toxicity, absorption, metabolism and toxicity.
  • Advaitabio: iPathwayGuide71 presents an advanced pathway analysis platform for high-throughput sequencing data.
  • LAZAR72 (Lazy Structure-Activity Relationships) Takes a chemical structure as input and provides several toxicity predictions. LAZAR is built on top of OpenTox
  • Toxtree73 Toxtree is a full-featured and flexible user-friendly open source application, which is able to estimate toxic hazard by applying a decision-tree approach. toxtree could be applied to datasets from various compatible file types. User-defined molecular structures are also supported—they could be entered by sMILEs, or by using the built-in 2D structure diagram editor. toxtree currently has the following plug-ins:
    • - Cramer rules and Cramer rules with extensions
    • - Verhaar scheme and modified verhaar scheme
    • - skin irritation prediction
    • - eye irritation prediction
    • - START biodegradation and persistence
    • - Benigni/Bossa rulebase for mutagenicity and carcinogenicity
    • - in vitro mutagenicity (Ames test) alerts by ISS
    • - structure alerts for the in vivo micronucleus assay in rodents (ISSMIC)
    • - structural alerts for functional group identification (ISSFUNC)
    • - structure alerts for identification of Michael acceptors
    • - structure alerts for skin sensitization reactivity domains
    • - DNA binding alerts
    • - Protein binding alerts
    • - Kroes thresholds of toxicological concern decision tree
    • - SMARTCyp: cytochrome P450-mediated drug metabolism and metabolites prediction
  • CAESAR74 QSAR models supporting the REACH legislation including bioconcentration, skin sensitization, carcinogenicity, and developmental toxicity.
  • ToxAlerts75 A web-based platform for collecting and storing toxicological structural alerts from literature and for virtual screening of chemical libraries to flag potentially toxic chemicals and compounds that can cause adverse side effects. An alert is uniquely identified by a SMARTS template, a toxicological endpoint, and a publication where the alert was described. Additionally, the system allows storing complementary information such as name, comments, and mechanism of action, as well as other data.
  • Online Chemical Database76 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. Includes chemical property predictions, ToxAlert screening, and optimization of different properties with Moloptimizer.
  • ToxRead77 Software to assist in making reproducible read-across evaluations. The software shows similar chemicals to the input chemical, structural alerts, and other relevant features in common between chemicals.
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