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Article ; Online: The coefficient of conformism of a correlative prediction (CCCP): Building up reliable nano-QSPRs/QSARs for endpoints of nanoparticles in different experimental conditions encoded via quasi-SMILES.

Toropova, Alla P / Toropov, Andrey A

2024 Volume 927, Page(s) 172119

Abstract: Simulation of the physicochemical and biochemical behavior of nanomaterials has its own specifics. However, the main goal of modeling for both traditional substances and nanomaterials is the same. This is an ecologic risk assessment. The universal ... ...

Abstract	Simulation of the physicochemical and biochemical behavior of nanomaterials has its own specifics. However, the main goal of modeling for both traditional substances and nanomaterials is the same. This is an ecologic risk assessment. The universal indicator of toxicity is the n-octanol/water partition coefficient. Mutagenicity indicates the possibility of future undesirable environmental effects, possibly greater than toxicity. Models have been proposed for the octanol/water distribution coefficient of gold nanoparticles and the mutagenicity of silver nanoparticles. Unlike the previous studies, here the models are built using an updated scheme, which includes two improvements. Firstly, the computing involves a new criterion for prediction potential, the so-called coefficient of conformism of a correlative prediction (CCCP); secondly, the Las Vegas algorithm is used to select the potentially most promising models from a group of models obtained by the Monte Carlo algorithm. Apparently, CCCP is a measure of the predictive potential (not only correlation). This can give an advantage in developing a model in comparison to using the classic determination coefficient. Likely, CCCP can be more informative than the classical determination coefficient. The Las Vegas algorithm is able to improve the model obtained by the Monte Carlo method.
MeSH term(s)	Quantitative Structure-Activity Relationship ; Algorithms ; Metal Nanoparticles ; Monte Carlo Method ; Models, Chemical ; Nanoparticles ; Risk Assessment/methods ; Silver
Chemical Substances	Silver (3M4G523W1G)
Language	English
Publishing date	2024-04-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2024.172119
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Article ; Online: Using the local symmetry in amino acids sequences of polypeptides to improve the predictive potential of models of their inhibitor activity.

Toropova, Alla P / Toropov, Andrey A

Amino acids

2023 Volume 55, Issue 10, Page(s) 1437–1445

Abstract: The minimal inhibitory concentrations (pMIC) are a valuable measure of the biological activity of polypeptides. Numerical data on the pMIC are necessary to systematize knowledge on polypeptides' biochemical behaviour. The model of negative decimal ... ...

Abstract	The minimal inhibitory concentrations (pMIC) are a valuable measure of the biological activity of polypeptides. Numerical data on the pMIC are necessary to systematize knowledge on polypeptides' biochemical behaviour. The model of negative decimal logarithm of pMIC of polypeptides in the form of a mathematical function of a sequence of amino acids is suggested. The suggested model is based on the so-called correlation weights of amino acids together with the correlation weights of fragments of local symmetry (FLS). Three kinds of the FLS are considered: (i) three-symbol fragments '…xyx…', (ii) four-symbol fragments '…xyyx…', and (iii) five-symbol fragments '…xyzyx…'. The models built using the Monte Carlo technique improved by applying the index of ideality of correlation (IIC) and correlation intensity index (CII).
MeSH term(s)	Amino Acids ; Quantitative Structure-Activity Relationship ; Software ; Peptides/pharmacology ; Monte Carlo Method
Chemical Substances	Amino Acids ; Peptides
Language	English
Publishing date	2023-09-14
Publishing country	Austria
Document type	Journal Article
ZDB-ID	1121341-3
ISSN	1438-2199 ; 0939-4451
ISSN (online)	1438-2199
ISSN	0939-4451
DOI	10.1007/s00726-023-03322-0
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Article ; Online: Does the accounting of the local symmetry fragments in quasi-SMILES improve the predictive potential of the QSAR models of toxicity toward tadpoles?

Toropova, Alla P / Toropov, Andrey A / Roncaglioni, Alessandra / Benfenati, Emilio

Toxicology mechanisms and methods

2024 , Page(s) 1–6

Abstract: Models of toxicity to tadpoles have been developed as single parameters based on special descriptors which are sums of correlation weights, molecular features, and experimental conditions. This information is presented by quasi-SMILES. Fragments of local ...

Abstract	Models of toxicity to tadpoles have been developed as single parameters based on special descriptors which are sums of correlation weights, molecular features, and experimental conditions. This information is presented by quasi-SMILES. Fragments of local symmetry (FLS) are involved in the development of the model and the use of FLS correlation weights improves their predictive potential. In addition, the index of ideality correlation (
Language	English
Publishing date	2024-04-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2081252-8
ISSN	1537-6524 ; 1537-6516 ; 1051-7235
ISSN (online)	1537-6524
ISSN	1537-6516 ; 1051-7235
DOI	10.1080/15376516.2024.2332617
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Article ; Online: Quasi-SMILES as a basis to build up models of endpoints for nanomaterials.

Toropova, Alla P / Toropov, Andrey A

Environmental technology

2022 Volume 44, Issue 28, Page(s) 4460–4467

Abstract: Simplified molecular input-line entry system (SMILES) is a format for representing of the molecular structure. Quasi-SMILES is an extended format for representing molecular structure data and some eclectic data, which in principle could be applied to ... ...

Abstract	Simplified molecular input-line entry system (SMILES) is a format for representing of the molecular structure. Quasi-SMILES is an extended format for representing molecular structure data and some eclectic data, which in principle could be applied to improve a model's predictive potential. Nano-quantitative structure-property relationships (nano-QSPRs) for energy gap (
MeSH term(s)	Monte Carlo Method ; Nanostructures ; Metal Nanoparticles ; Molecular Structure ; Quantitative Structure-Activity Relationship ; Oxides ; Software
Chemical Substances	Oxides
Language	English
Publishing date	2022-06-30
Publishing country	England
Document type	Journal Article
ISSN	1479-487X
ISSN (online)	1479-487X
DOI	10.1080/09593330.2022.2093655
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Article ; Online: Nanomaterials: Quasi-SMILES as a flexible basis for regulation and environmental risk assessment.

Toropova, Alla P / Toropov, Andrey A

The Science of the total environment

2022 Volume 823, Page(s) 153747

Abstract: Basic principles and problems of the systematization of data on nanomaterials are discussed. The eclectic character of nanomaterials is defined as the key difference between nanomaterials and traditional substances. The quasi-SMILES technique is ... ...

Abstract	Basic principles and problems of the systematization of data on nanomaterials are discussed. The eclectic character of nanomaterials is defined as the key difference between nanomaterials and traditional substances. The quasi-SMILES technique is described and discussed. The possible role of the approach is bridging between experimentalists and developers of models for endpoints related to nanomaterials. The use of models on the possible impact of nanomaterials on the environment and human health has been collected and compared. The new criteria of the predictive potential for the above models are discussed. The advantage of the statistical criteria sensitive simultaneously to both the correlation coefficient and the root mean square error noted. The rejection of the border between the effect of the biochemical reality of substances at a molecular level and the effect of experiment conditions at the macro level gives the possibility to develop models that are epistemologically more reliable in the comparison with traditional models based exclusively on the molecular structure-biological activity interdependence (without taking into account experimental conditions). Models of the physicochemical and biochemical behaviour of nanomaterials are necessary in order to develop and apply new industrial achievements, everyday comfort species, medicine, cosmetics, and foods without negative effects on ecology and human health. The CORAL (abbreviation CORrelation And Logic) software provides the user with the possibility to build up nano-QSAR models as a mathematical function of so-called correlation weights of fragments of quasi-SMILES. These models are built up via the Monte Carlo method. Apparently, the quasi-SMILES is a universal representation of nano-reality since there is no limitation to choose the list of eclectic data able to have an impact on nano-phenomena. This paradigm is a convenient language to the conversation of experimentalists and developers of models for nano-phenomena.
MeSH term(s)	Models, Chemical ; Molecular Structure ; Monte Carlo Method ; Nanostructures/chemistry ; Nanostructures/standards ; Quantitative Structure-Activity Relationship ; Risk Assessment ; Software
Language	English
Publishing date	2022-02-09
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.153747
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Article ; Online: In Silico Simulation of Impacts of Metal Nano-Oxides on Cell Viability in THP-1 Cells Based on the Correlation Weights of the Fragments of Molecular Structures and Codes of Experimental Conditions Represented by Means of Quasi-SMILES.

Toropova, Alla P / Toropov, Andrey A / Fjodorova, Natalja

International journal of molecular sciences

2023 Volume 24, Issue 3

Abstract: A simulation of the effect of metal nano-oxides at various concentrations (25, 50, 100, and 200 milligrams per millilitre) on cell viability in THP-1 cells (%) based on data on the molecular structure of the oxide and its concentration is proposed. We ... ...

Abstract	A simulation of the effect of metal nano-oxides at various concentrations (25, 50, 100, and 200 milligrams per millilitre) on cell viability in THP-1 cells (%) based on data on the molecular structure of the oxide and its concentration is proposed. We used a simplified molecular input-line entry system (SMILES) to represent the molecular structure. So-called quasi-SMILES extends usual SMILES with special codes for experimental conditions (concentration). The approach based on building up models using quasi-SMILES is self-consistent, i.e., the predictive potential of the model group obtained by random splits into training and validation sets is stable. The Monte Carlo method was used as a basis for building up the above groups of models. The CORAL software was applied to building the Monte Carlo calculations. The average determination coefficient for the five different validation sets was R
MeSH term(s)	Humans ; Molecular Structure ; THP-1 Cells ; Cell Survival ; Quantitative Structure-Activity Relationship ; Computer Simulation ; Software ; Oxides ; Monte Carlo Method
Chemical Substances	Oxides
Language	English
Publishing date	2023-01-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24032058
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Article ; Online: The system of self-consistent models for pesticide toxicity to

Toropov, Andrey A / Toropova, Alla P / Roncaglioni, Alessandra / Benfenati, Emilio

Toxicology mechanisms and methods

2023 Volume 33, Issue 7, Page(s) 578–583

Abstract: Quantitative structure-property/activity relationships (QSPRs/QSARs) are a tool of modern theoretical and computational chemistry. The self-consistent model system is both a method to build up a group of QSPR/QSAR models and an approach to checking the ... ...

Abstract	Quantitative structure-property/activity relationships (QSPRs/QSARs) are a tool of modern theoretical and computational chemistry. The self-consistent model system is both a method to build up a group of QSPR/QSAR models and an approach to checking the reliability of these models. Here, a group of models of pesticide toxicity toward
MeSH term(s)	Animals ; Daphnia ; Reproducibility of Results ; Software ; Monte Carlo Method ; Quantitative Structure-Activity Relationship ; Pesticides/toxicity
Chemical Substances	Pesticides
Language	English
Publishing date	2023-05-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2081252-8
ISSN	1537-6524 ; 1537-6516 ; 1051-7235
ISSN (online)	1537-6524
ISSN	1537-6516 ; 1051-7235
DOI	10.1080/15376516.2023.2197487
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Article ; Online: Using the Correlation Intensity Index to Build a Model of Cardiotoxicity of Piperidine Derivatives.

Toropova, Alla P / Toropov, Andrey A / Roncaglioni, Alessandra / Benfenati, Emilio

Molecules (Basel, Switzerland)

2023 Volume 28, Issue 18

Abstract: The assessment of cardiotoxicity is a persistent problem in medicinal chemistry. Quantitative structure-activity relationships (QSAR) are one possible way to build up models for cardiotoxicity. Here, we describe the results obtained with the Monte Carlo ... ...

Abstract	The assessment of cardiotoxicity is a persistent problem in medicinal chemistry. Quantitative structure-activity relationships (QSAR) are one possible way to build up models for cardiotoxicity. Here, we describe the results obtained with the Monte Carlo technique to develop hybrid optimal descriptors correlated with cardiotoxicity. The predictive potential of the cardiotoxicity models (
MeSH term(s)	Humans ; Cardiotoxicity/etiology ; Chemistry, Pharmaceutical ; Monte Carlo Method ; Piperidines ; Quantitative Structure-Activity Relationship
Chemical Substances	Piperidines
Language	English
Publishing date	2023-09-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules28186587
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Article ; Online: Can the Monte Carlo method predict the toxicity of binary mixtures?

Toropova, Alla P / Toropov, Andrey A

Environmental science and pollution research international

2021 Volume 28, Issue 29, Page(s) 39493–39500

Abstract: Risk assessment of toxicants mainly is a result of experiments with single substances. However, toxicity in natural ecosystems typically does not result from single toxicant exposure but is rather a result of exposure to mixtures of toxicants. It is not ... ...

Abstract	Risk assessment of toxicants mainly is a result of experiments with single substances. However, toxicity in natural ecosystems typically does not result from single toxicant exposure but is rather a result of exposure to mixtures of toxicants. It is not surprising a mixture of toxicity is a subject of eco-toxicological interest for several decades. A quantitative structure-activity relationships (QSAR)-based approach is an attractive approach to assessing the joint effects in the binary mixtures. The validity of the proposed approach was demonstrated by comparing the predicted values against the experimentally determined values. Simplified molecular input-line entry system (SMILES) is used for the representation of the molecular structures of components of two-component mixtures to build up QSAR. The SMILES-based models are improving if the Monte Carlo optimization aimed to define 2D-optimal descriptors apply the so-called index of ideality of correlation (IIC), which is a mathematical function of both the correlation coefficient and mean absolute error calculated for the positive and negative difference between observed and calculated values of toxicity. The average statistical quality of these models (for the validation set) is n=25, R
MeSH term(s)	Ecosystem ; Molecular Structure ; Monte Carlo Method ; Quantitative Structure-Activity Relationship ; Software
Language	English
Publishing date	2021-03-23
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-021-13460-1
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Article ; Online: Quasi-SMILES as a basis for the development of models for the toxicity of ZnO nanoparticles.

Toropov, Andrey A / Toropova, Alla P

The Science of the total environment

2021 Volume 772, Page(s) 145532

Abstract: The application of nanomaterials is expanding. Therefore, it is necessary to investigate the relationship between the structure and toxicity of different nanomaterials. Quasi-SMILES is a line of symbols which are codes of corresponding conditions of ... ...

Abstract	The application of nanomaterials is expanding. Therefore, it is necessary to investigate the relationship between the structure and toxicity of different nanomaterials. Quasi-SMILES is a line of symbols which are codes of corresponding conditions of experiments aimed to estimate the toxicity of ZnO nanoparticles towards the rat via intraperitoneal injections. By means of the Monte Carlo method, the so-called correlation weights for fragments of quasi-SMILES can be calculated. Having the numerical data on the correlation weights one can build up a one-variable model for the toxicity. The checking up of the approach with five random splits of all available data on results of thirty-six experiments into a sub-system of training and sub-system of validation has confirmed the significance of the statistical quality of models obtained with the above approach. The average determination coefficient equal to 0.957 (dispersion 0.010) and average root mean square error equal to 7.25 [mg/kg] (dispersion 0.59 [mg/kg]).
MeSH term(s)	Animals ; Monte Carlo Method ; Nanoparticles/toxicity ; Quantitative Structure-Activity Relationship ; Rats ; Software ; Zinc Oxide/toxicity
Chemical Substances	Zinc Oxide (SOI2LOH54Z)
Language	English
Publishing date	2021-02-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2021.145532
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