Literature DB >> 27476736

QSAR Modeling is not "Push a Button and Find a Correlation": A Case Study of Toxicity of (Benzo-)triazoles on Algae.

Paola Gramatica1, Stefano Cassani2, Partha Pratim Roy2,3, Simona Kovarich2, Chun Wei Yap4, Ester Papa2.   

Abstract

A case study of toxicity of (benzo)triazoles ((B)TAZs) to the algae Pseudokirchneriella subcapitata is used to discuss some problems and solutions in QSAR modeling, particularly in the environmental context. The relevance of data curation (not only of experimental data, but also of chemical structures and input formats for the calculation of molecular descriptors), the crucial points of QSAR model validation and the potential application for new chemicals (internal robustness, exclusion of chance correlation, external predictivity, applicability domain) are described, while developing MLR-OLS models based on molecular descriptors, calculated by various QSAR software tools (commercial DRAGON, free PaDEL-Descriptor and QSPR-THESAURUS). Additionally, the utility of consensus models is highlighted. This work summarizes a methodology for a rigorous statistical approach to obtain reliable QSAR predictions, also for a large number of (B)TAZs in the ECHA preregistration list of REACH (even if starting from limited experimental data availability), and has evidenced some ambiguities and discrepancies related to SMILES notations from different databases; furthermore it highlighted some general problems related to QSAR model generation and was useful in the implementation of the PaDEL-Descriptor software.
Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Entities:  

Keywords:  Chemical structure pitfalls; Molecular descriptors; QSAR tutorial; REACH; SMILES; Triazole algae toxicity; Validation

Year:  2012        PMID: 27476736     DOI: 10.1002/minf.201200075

Source DB:  PubMed          Journal:  Mol Inform        ISSN: 1868-1743            Impact factor:   3.353


  19 in total

1.  Geometry optimization method versus predictive ability in QSPR modeling for ionic liquids.

Authors:  Anna Rybinska; Anita Sosnowska; Maciej Barycki; Tomasz Puzyn
Journal:  J Comput Aided Mol Des       Date:  2016-02-01       Impact factor: 3.686

2.  Structure-activity analysis of harmful algae inhibition by congeneric compounds: case studies of fatty acids and thiazolidinediones.

Authors:  Haomin Huang; Xi Xiao; Jiyan Shi; Yingxu Chen
Journal:  Environ Sci Pollut Res Int       Date:  2014-02-25       Impact factor: 4.223

3.  Combined molecular docking and QSAR study of fused heterocyclic herbicide inhibitors of D1 protein in photosystem II of plants.

Authors:  Simona Funar-Timofei; Ana Borota; Luminita Crisan
Journal:  Mol Divers       Date:  2017-03-16       Impact factor: 2.943

4.  A novel approach for assessment of antitrypanosomal activity of sesquiterpene lactones through additive and non-additive molecular structure parameters.

Authors:  Mohammad Hossein Keshavarz; Zeinab Shirazi; Faezeh Sayehvand
Journal:  Mol Divers       Date:  2022-07-17       Impact factor: 3.364

Review 5.  From Traditional Ethnopharmacology to Modern Natural Drug Discovery: A Methodology Discussion and Specific Examples.

Authors:  Stergios Pirintsos; Athanasios Panagiotopoulos; Michalis Bariotakis; Vangelis Daskalakis; Christos Lionis; George Sourvinos; Ioannis Karakasiliotis; Marilena Kampa; Elias Castanas
Journal:  Molecules       Date:  2022-06-24       Impact factor: 4.927

6.  Comparative performance of descriptors in a multiple linear and Kriging models: a case study on the acute toxicity of organic chemicals to algae.

Authors:  Gulcin Tugcu; H Birkan Yilmaz; Melek Türker Saçan
Journal:  Environ Sci Pollut Res Int       Date:  2014-06-21       Impact factor: 4.223

7.  In silico local QSAR modeling of bioconcentration factor of organophosphate pesticides.

Authors:  Purusottam Banjare; Balaji Matore; Jagadish Singh; Partha Pratim Roy
Journal:  In Silico Pharmacol       Date:  2021-04-04

8.  Exploring the Prominent and Concealed Inhibitory Features for Cytoplasmic Isoforms of Hsp90 Using QSAR Analysis.

Authors:  Magdi E A Zaki; Sami A Al-Hussain; Syed Nasir Abbas Bukhari; Vijay H Masand; Mithilesh M Rathore; Sumer D Thakur; Vaishali M Patil
Journal:  Pharmaceuticals (Basel)       Date:  2022-03-01

9.  Combined Ligand/Structure-Based Virtual Screening and Molecular Dynamics Simulations of Steroidal Androgen Receptor Antagonists.

Authors:  Yuwei Wang; Rui Han; Huimin Zhang; Hongli Liu; Jiazhong Li; Huanxiang Liu; Paola Gramatica
Journal:  Biomed Res Int       Date:  2017-02-15       Impact factor: 3.411

10.  Modeling adsorption of brominated, chlorinated and mixed bromo/chloro-dibenzo-p-dioxins on C60 fullerene using Nano-QSPR.

Authors:  Piotr Urbaszek; Agnieszka Gajewicz; Celina Sikorska; Maciej Haranczyk; Tomasz Puzyn
Journal:  Beilstein J Nanotechnol       Date:  2017-03-31       Impact factor: 3.649

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