QSAR models for ACE-inhibitor activity of tri-peptides based on representation of the molecular structure by graph of atomic orbitals and SMILES

The rodent carcinogenicity dataset was compiled from the Carcinogenic Potency Database (CPDBAS) and was applied for the classification of quantitative structure-activity relationship (QSAR) models for the prediction of carcinogenicity based on the counter-propagation artificial neural network (CP ANN) algorithm. The models were developed within EU-funded project CAESAR for regulatory use. The dataset contains the following information: common information about chemicals (ID, chemical name, and their CASRN), molecular structure information (SDF files and SMILES), and carcinogenic (toxicological) properties information: carcinogenic potency (TD50_Rat_mg; carcinogen/noncarcinogen) and structural alert (SA) for carcinogenicity based on mechanistic data. Molecular structure information was used to get chemometrics information to calculate molecular descriptors (254 MDL and 784 Dragon descriptors), which were further used in predictive QSAR modeling. The dataset presented in the paper can be used in future research in oncology, ecology, or chemicals' risk assessment.

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Comparison of QSAR models of anti-HIV-1 potencies based on labeled hydrogen filled graph and graph of atomic orbitals

Journal of Molecular Structure THEOCHEM ◽

10.1016/j.theochem.2003.08.127 ◽

2003 ◽

Vol 640 (1-3) ◽

pp. 175-181 ◽

Cited By ~ 7

Author(s):

Andrey A Toropov ◽

Alla P Toropova ◽

Igor V Nesterov ◽

Ozod M Nabiev

Keyword(s):

Atomic Orbitals ◽

Qsar Models ◽

Anti Hiv ◽

Hiv 1

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The analysis of structure-anticancer and antiviral activity relationships for macrocyclic pyridinophanes and their analogues on the basis of 4D QSAR models (simplex representation of molecular structure).

Acta Biochimica Polonica ◽

10.18388/abp.2002_3832 ◽

2002 ◽

Vol 49 (1) ◽

pp. 157-168 ◽

Cited By ~ 22

Author(s):

Victor E Kuz'min ◽

Anatoly G Artemenko ◽

Victor P Lozitsky ◽

Eugene N Muratov ◽

Alla S Fedtchouk ◽

...

Keyword(s):

Molecular Structure ◽

Biological Activity ◽

Antiviral Activity ◽

Direct Synthesis ◽

Antiviral Agents ◽

Structural Models ◽

Fourth Dimension ◽

Molecular Fragments ◽

Qsar Models ◽

Fixed Structure

A new 4D-QSAR approach has been considered. For all investigated molecules the 3D structural models have been created and the set of conformers (fourth dimension) have been used. Each conformer is represented as a system of different simplexes (tetratomic fragments of fixed structure, chirality and symmetry). The investigation of influence of molecular structure of macrocyclic pyridinophanes, their analogues and certain other compounds on anticancer and antiviral (anti-influenza, antiherpes and antiadenovirus) activity has been carried out by means of the 4D-QSAR. Statistic characteristics for QSAR of PLS (partial least squares) models are satisfactory (R = 0.92-0.97; CVR = 0.63-0.83). Molecular fragments increasing and decreasing biological activity were defined. This information may be useful for design, and direct synthesis of novel anticancer and antiviral agents.

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Hybrid Atomic Orbitals in Organic Chemistry. Part 2: Critique of Practical Aspects

10.26434/chemrxiv.7763147 ◽

2019 ◽

Author(s):

Guy Lamoureux ◽

J. F. Ogilvie

Keyword(s):

Organic Chemistry ◽

Molecular Structure ◽

Critical Survey ◽

Atomic Orbitals ◽

Hybrid Orbitals

The importance of hybrid atomic orbitals, in both general and organic chemistry, is reviewed. Every contemporary textbook of organic chemistry introduces the sp3, sp2, sp model, but the suitability of these hybrid orbitals for use in the teaching of molecular structure has been increasingly questioned. Based on a critical survey of the literature, we submit seven practical criteria that deprecate the use of hybrid orbitals in a pedagogical context. We suggest how the teaching of organic chemistry without hybrid orbitals will provide students with an enhanced education.

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Structural, Physicochemical and Stereochemical Interpretation of QSAR Models Based on Simplex Representation of Molecular Structure

Challenges and Advances in Computational Chemistry and Physics - Advances in QSAR Modeling ◽

10.1007/978-3-319-56850-8_4 ◽

2017 ◽

pp. 107-147 ◽

Cited By ~ 1

Author(s):

P. Polishchuk ◽

E. Mokshyna ◽

A. Kosinskaya ◽

A. Muats ◽

M. Kulinsky ◽

...

Keyword(s):

Molecular Structure ◽

Qsar Models

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QSAR Study of Artemisinin Analogues as Antimalarial Drugs by Neural Network and Replacement Method

Drug Research ◽

10.1055/s-0043-108553 ◽

2017 ◽

Vol 67 (08) ◽

pp. 476-484 ◽

Cited By ~ 2

Author(s):

Fatemeh Abbasitabar ◽

Vahid Zare-Shahabadi

Keyword(s):

Neural Network ◽

Molecular Structure ◽

Antimalarial Activity ◽

General Regression Neural Network ◽

Relative Standard Error ◽

Qsar Study ◽

Test Set ◽

Replacement Method ◽

Relative Standard ◽

Qsar Models

AbstractQuantitative structure–activity relationship (QSAR) models were derived for 179 analogues of artemisinin, a potent antimalarial agent. Molecular descriptors derived solely from molecular structure were used to represent molecular structure. Utilizing replacement method, a subset of 11 descriptors was selected. General regression neural network (GRNN) was used to construct the nonlinear QSAR models in all stages of study. The relative standard error percent in antimalarial activity predictions for the training set by the application of cross-validation (RMSE-CV) was 0.43, and for test set (RMSEtest) was 0.51. GRNN analysis yielded predicted activities in the excellent agreement with the experimentally obtained values (R2training = 0.967 and R2test = 0.918). The mean absolute error for the test set was computed as 0.4115.

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ORBITALS IN GENERAL CHEMISTRY, PART II: MATHEMATICAL REALITIES

Química Nova ◽

10.21577/0100-4042.20170664 ◽

2020 ◽

Author(s):

Guy Lamoureux ◽

John Ogilvie

Keyword(s):

Molecular Structure ◽

General Chemistry ◽

Quantum Mechanics ◽

Constant Amplitude ◽

Qualitative Explanation ◽

Mathematical Functions ◽

Atomic Orbitals ◽

Two Factors

In Part II of a three-part series, we discuss two factors absent from textbooks of general chemistry that are important in a discussion of teaching orbitals. First, atomic orbitals are shown systematically to comprise algebraic formulae in coordinates of not one but four sets (spherical polar, paraboloidal, ellipsoidal, spheroconical coordinates). Each formula has its corresponding shape as a surface of constant amplitude; some visual examples are provided. Second, the argument that molecular structure is incompatible with quantum mechanics is presented. Despite the utility of orbitals as mathematical functions in various calculations, they are intrinsically complicated for the traditional purpose of qualitative explanation of molecular structure.

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