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Structure–Toxicity Relationships for Aliphatic Compounds Based on Correlation Weighting of Local Graph Invariants

Andrey Toropov, Pablo Duchowicz, Eduardo Castro
2003 International Journal of Molecular Sciences  
Quantitative Structure-Activity Relationships based on molecular descriptors calculated with Correlation Weights of Local Graph Invariants were developed to model the toxicity of aliphatic compounds to  ...  The relationships were computed on the basis of Labeled Hydrogen-Filled Graphs and correlation weights were obtained by an optimization to render as large as possible correlation coefficients between log  ...  Acknowledgement Authors would like to thank several valuable comments and suggestions which have been useful to improve the final version of this paper.  ... 
doi:10.3390/i4050272 fatcat:4klcgldj4ngb7eqklokhjlxbsm

OCWLGI Descriptors: Theory and Praxis

Andrey Toropov, Alla Toropova, Emilio Benfenati, Giuseppina Gini
2013 Current Computer - Aided Drug Design  
The Monte Carlo method optimization of the correlation weights of local and global invariants (OCWLGI) of molecular graphs is used as the principle for building up descriptors which are discussed in this  ...  Keywords: Global invariant, local invariant, Monte Carlo method, optimization of correlation weights of local and global invariants of graph (OCWLGI), quantitative structure-property relationships, QSPR  ...  This paper is dedicated to Professor Milan Randi on the occasion of his 80 birthday.  ... 
doi:10.2174/1573409911309020007 pmid:23700994 fatcat:o7mn5dt4k5cjhd5zkq3gybkily

A comparative study of molecular similarity, statistical, and neural methods for predicting toxic modes of action

Subhash C. Basak, Gregory D. Grunwald, George E. Host, Gerald J. Niemi, Steven P. Bradbury
1998 Environmental Toxicology and Chemistry  
In this paper, we used molecular similarity, neural networks, and discriminant analysis methods to predict acute toxic modes of action for a set of 283 chemicals.  ...  Quantitative structure-activity relationship (QSAR) models are routinely used in predicting toxicologic and ecotoxicologic effects of untested chemicals.  ...  Mention of models or modeling approaches does not constitute endorsement on the part of the U.S. EPA.  ... 
doi:10.1002/etc.5620170611 fatcat:md25vppnmffs7aqupjo2fs5zda

QSPR modeling aqueous solubility of polychlorinated biphenyls by optimization of correlation weights of local and global graph invariants

Eduardo Castro, Andrey Toropov, Alexandra Nesterova, Ozad Nabiev
2004 Open Chemistry  
Morgan extended connectivity and nearest neighboring codes have been used as local graph invariants. The number of chlorine atoms in biphenyls has been employed as a global graph invariant.  ...  Present results show that taking into account correlation weights of global invariants gives quite reasonable improvement of statistical characteristics for the prediction of aqueous solubilities of polychlorinated  ...  Acknowledgment Authors thanks valuable comments made by two anonymous referees which have been very helpful to improve the final version of this article.  ... 
doi:10.2478/bf02476204 fatcat:fv7mly2wm5hwdganzaygkzm3yu

Nano-QSAR: Model of mutagenicity of fullerene as a mathematical function of different conditions

Alla P. Toropova, Andrey A. Toropov, Aleksandar M. Veselinović, Jovana B. Veselinović, Emilio Benfenati, Danuta Leszczynska, Jerzy Leszczynski
2016 Ecotoxicology and Environmental Safety  
the optimal descriptors calculated with the Monte Carlo method a mathematical 17 model of these endpoints has been built up.  ...  In contrast to the traditional SMILES which are 21 representation of molecular structure, the quasi-SMILES are representation of conditions by 22 sequence of symbols.  ...  QSPR Modeling of lipid-water partition coefficient by 264 optimization of correlation weights of local graph invariants. J. Chem. Inf. Comput.  ... 
doi:10.1016/j.ecoenv.2015.09.038 pmid:26452192 fatcat:ri4bn4nnlzfbrlpwudj75tfxfa

Validation of counter propagation neural network models for predictive toxicology according to the OECD principles: a case study

M. Vračko, V. Bandelj, P. Barbieri, E. Benfenati, Q. Chaudhry, M. Cronin, J. Devillers, A. Gallegos, G. Gini, P. Gramatica, C. Helma, P. Mazzatorta (+7 others)
2006 SAR and QSAR in environmental research (Print)  
The OECD has proposed five principles for validation of QSAR models used for regulatory purposes.  ...  The study is based on a counter propagation network model that has been built using toxicity data in fish fathead  ...  used Morgan extended connectivity and nearest neighboring codes as local graph invariants in a study of 51 aldehydes.  ... 
doi:10.1080/10659360600787650 pmid:16815767 fatcat:q2ke2yk6srd6xowwk72l6xza2a

Predictive toxicology using QSAR : A perspective

Supratik Kar, Kunal Roy
2010 Zenodo  
assessments of chemicals and drug-induced toxicities and in safety evaluations.  ...  The use of QSAR modelling for toxicological predictions would help to determine the potential adverse effects of chemical entities in risk assessment, chemical screening, and priority setting.  ...  Acknowledgement Financial assistance from the Ministry of Human Resource Development, Government of India, New Delhi in the form of a scholarship to SK is thankfully acknowledged.  ... 
doi:10.5281/zenodo.5805066 fatcat:n75jlitmrfem3k53jbvsmjqc6a

Exploration of Chemical Space by Machine Learning

Sergey Sosnin
and Data Science and Engineering, Skolkovo Institute of Science and Technology (Skoltech).  ...  Submitted to the Center for Computational and Data-Intensive Science and Engineering and Innovation on September 2020, in partial fulfillment of the requirements for the Doctoral Program in Computational  ...  Invariants of these graphs are called molecular descriptors or descriptors, etc.  ... 
doi:10.6084/m9.figshare.14160683.v1 fatcat:qqqvebwf3vbu5c2nte6a4uiowe

Hyperspectral Imaging of Macroinvertebrates—a Pilot Study for Detecting Metal Contamination in Aquatic Ecosystems

Johanna Salmelin, Ilkka Pölönen, Hannu-Heikki Puupponen, Heikki Hämäläinen, Anna K. Karjalainen, Ari Väisänen, Kari-Matti Vuori
2018 Water, Air and Soil Pollution  
39 40 Keywords: Aquatic insect larvae; cadmium toxicity; Fabry-Perot interferometer; hyperspectral 41 imaging; metal pollution 42 43  ...  24 The applicability of spectral analysis in detection of freshwater metal contamination was assessed 25 by developing and testing a novel hyperspectral imaging (HSI) application for aquatic insect 26  ...  Although the larval tissue 31 Cd concentrations correlated positively with actual water concentrations, the toxicity response of 32 larvae i.e. frequency of gill abnormalities did not differ among the  ... 
doi:10.1007/s11270-018-3963-2 fatcat:li4jldl6l5cevmf7tnd23yskrm

QSAR Modeling: Where Have You Been? Where Are You Going To?

Artem Cherkasov, Eugene N. Muratov, Denis Fourches, Alexandre Varnek, Igor I. Baskin, Mark Cronin, John Dearden, Paola Gramatica, Yvonne C. Martin, Roberto Todeschini, Viviana Consonni, Victor E. Kuz'min (+8 others)
2014 Journal of Medicinal Chemistry  
We hope that this Perspective will help communications between computational and experimental chemists towards collaborative development and use of QSAR models.  ...  Throughout this discussion, we provide guidelines for QSAR development, validation, and application, which are summarized in best practices for building rigorously validated and externally predictive QSAR  ...  several new classes of related graph invariants. 44 Single indices derived from a molecular graph are usually called topological indices.  ... 
doi:10.1021/jm4004285 pmid:24351051 pmcid:PMC4074254 fatcat:bzjqonekb5gkhojb2wpcvyn2l4

Principles of QSAR Modeling

Paola Gramatica
2020 International Journal of Quantitative Structure-Property Relationships  
The commented approach is the "predictive" one, based on chemometrics, and is usefully applied to the prioritization of environmental pollutants.  ...  can be useful also for other QSAR methods.  ...  graph for applicability domain on training (yellow), prediction set (blue) and chemicals with unknown experimental value (red) Figure 4 . 4 Definition of the Aquatic Toxicity Index (ATI) of pharmaceuticals  ... 
doi:10.4018/ijqspr.20200701.oa1 fatcat:ozmjtlkubnfxtg3jfzy3bpy4jm

AI for predicting chemical-effect associations at the universe level - deepFPlearn [article]

Jana Schor, Patrick Scheibe, Matthias Berndt, Wibke Busch, Chih Lai, Jörg Hackermüller
2021 bioRxiv   pre-print
Here, we present the ready-to-use and stand-alone program deepFPlearn that predicts the association between chemical structures and effects on the gene/pathway level using deep learning.  ...  We show good performance values for our trained models, and demonstrate that our program can predict meaningful associations of chemicals and effects beyond the training range due to the application of  ...  on biological activity. 2D QSAR uses descriptors derived from the 2Dstructure graph of a molecule that are identical for isomorphic graphs (graph invariants) [23] .  ... 
doi:10.1101/2021.06.24.449697 fatcat:4npuaiealbfobfa27bchijzjv4

Sustainable Marine Ecosystems: Deep Learning for Water Quality Assessment and Forecasting

A. Fernandez Gambin, E. Angelats, J. Soriano Gonzalez, M. Miozzo, P. Dini
2021 IEEE Access  
Finally, the BP algorithm is used to fine-tune the weight optimization and attain the final DBN model [32] .  ...  Pearson's correlation coefficient is used to obtain the correlation priors between pH, water temperature, and other water quality parameters to be used in the prediction model.  ...  In the last years, he has investigated the potential of using multispectral imagery, from RPAS or Sentinel-2, together with advanced processing techniques for the detection of archaeological non-superficial  ... 
doi:10.1109/access.2021.3109216 fatcat:e4mubouhprcm3l2kanxjtrir54

In Silicoanalysis of perturbed steroidogenesis and gonad growth in fathead minnows (P. promelas) exposed to 17α-ethynylestradiol

David Hala, Lene H. Petersen, Dalma Martinović, Duane B. Huggett
2015 Systems Biology in Reproductive Medicine  
The authors report no declarations of interest.  ...  into mechanisms of toxicity [Volz et al. 2011 ].  ...  Liver and gonad tissues were subsequently excised and weighed for determination of hepatosomatic and gonadosomatic indices (using formula: (tissue weight/(whole body weight -tissue weight)) * 100) [Harries  ... 
doi:10.3109/19396368.2015.1035817 pmid:25910217 fatcat:tsk4hznztbfpfhkwret7w3uf2q

Molecular Design QSTR Study on Aquatic Toxicity Against Poecilia reticulata and Tetrahymena pyriformis Using Topological Indices BioChem Press QSTR Study on Aquatic Toxicity Against Poecilia reticulata and Tetrahymena pyriformis Using Topological Indices #

Adina Costescu, Mircea Diudea, Adina Costescu, Mircea Diudea
2006 Diudea Internet Electronic Journal of Molecular Design   unpublished
Topological indices are used to relate the chemical structures to their toxic activity against aquatic organisms.  ...  This procedure can be used to approach the aquatic toxicity and to select the appropriate model for new chemical compounds.  ...  Optimization of correlation weights of local graph invariants was used by Toropov et al. [24] to predict the aquatic toxicity. Seward et al.  ... 
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