QSPR/QSAR Analysis Using SMILES and Quasi-SMILES

Alla P. Toropova, Andrey A. Toropov

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English

Springer International Publishing AG
11 June 2023

Series: Challenges and Advances in Computational Chemistry and Physics

This contributed volume overviews recently presented approaches for carrying out QSPR/QSAR analysis by using a simplifying molecular input-line entry system (SMILES) to represent the molecular structure. In contrast to traditional SMILES, quasi-SMILES is a sequence of special symbols-codes that reflect molecular features and codes of experimental conditions. SMILES and quasi-SMILES serve as a basis to develop QSPR/QSAR as well Nano-QSPR/QSAR via the Monte Carlo calculation that provides the so-called optimal descriptors for QSPR/QSAR models. The book presents a reliable technology for developing Nano-QSPR/QSAR while it also includes the description of the algorithms of the Monte Carlo optimization. It discusses the theory and practice of the technique of variational authodecoders (VAEs) based on SMILES and analyses in detail the index of ideality of correlation (IIC) and the correlation intensity index (CII) which are new criteria for the predictive potential of the model. The mathematical apparatus used is simple so that students of relevant specializations can easily follow. This volume is a valuable contribution to the field and will be of great interest to developers of models of physicochemical properties and biological activity, chemical technologists, and toxicologists involved in the area of drug design.

Edited by: Alla P. Toropova, Andrey A. Toropov
Imprint: Springer International Publishing AG
Country of Publication: Switzerland
Edition: 2023 ed.
Volume: 33
Dimensions: Height: 235mm, Width: 155mm,
Weight: 893g
ISBN: 9783031284007
ISBN 10: 3031284003
Series: Challenges and Advances in Computational Chemistry and Physics
Pages: 467
Publication Date: 11 June 2023
Audience: Professional and scholarly , Undergraduate
Format: Hardback
Publisher's Status: Active

Part I - Theoretical conceptions.- Fundamentals of mathematical modeling of chemicals through QSPR/QSAR.- Molecular descriptors in QSPR/QSAR modeling.- Application of SMILES to cheminformatics and generation of optimum SMILES descriptors using CORAL software.- Part II - SMILES based descriptors.- All SMILES Variational Autoencoder for Molecular Property Prediction and Optimization.- SMILES based bioactivity descriptors to model the anti-Dengue virus activity: A case study.- Part III - SMILES for QSPR/QSAR with optimal descriptors.- QSPR models for prediction of redox potentials using optimal descriptors.- Building up QSPR for polymers endpoints by using SMILES-based optimal descriptors.- Part IV - Quasi-SMILES for QSPR/QSAR.- Quasi-SMILES based QSPR/QSAR modeling.- Quasi-SMILES Based Mathematical Model for the Prediction of Percolation Threshold for Conductive Polymer Composites.- On the possibility to build up the QSAR model of different kinds of inhibitory activity for a large list of Human Intestinal Transporter using quasi-SMILES.- Quasi-SMILES as a tool for peptide QSAR modelling.- Part V - SMILES and quasi-SMILES for QSPR/QSAR.- SMILES and quasi-SMILES descriptors in QSAR/QSPR modeling of diverse materials properties in safety and environment application.- SMILES and quasi-SMILES in QSAR Modeling for Prediction of Physicochemical and Biochemical Properties.- Part VI - Possible ways of nano-QSPR/nano-QSAR evolution.- The CORAL software as a tool to develop models for nanomaterials’ endpoints.- Employing Quasi-SMILES notation in development of nano-QSPR models for nanofluids.- Part VII - Possible ways of QSPR/QSAR evolution in the future.- On complementary approaches of assessing the predictive potential of QSPR/QSAR-models.- CORAL: Predictions of Quality of Rice based on Retention index using a combination of Correlation intensity index and Consensus modelling.

Alla P. Toropova is a researcher from Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy. Her main direction of research activity is establishing quantitative structure-property/activity relationships (QSPRs/QSARs) for inorganic and metalorganic compounds. She has published about 280 papers in international journals dedicated to QSPR/QSAR analysis. She took part in the development and evolution of so-called optimal descriptors that were calculated with a simplified molecular input-line entry system (SMILES). In addition, she collaborated on developing a new approach to the QSPR/QSAR analysis based on so-called quasi-SMILES. She is the website developer(http://www.insilico.eu/coral) for the CORAL software that implements conceptions of the Monte Carlo optimization of optimal descriptors calculated with SMILES and quasi-SMILES. Andrey A. Toropov is a researcher from Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy. His research activity is dedicated to quantitative structure-property/activity relationships (QSPRs/QSARs). He is co-author of about 360 papers in international journals devoted to QSPR/QSAR analysis. He is the developer of CORAL software that is applied to building up QSPR/QSAR models for different endpoints. His current activity is dedicated to developing the system of quasi-SMILES as input data for the CORAL software (http://www.insilico.eu/coral). It can become a new approach for building up QSPR/QSAR for polymers, peptides, and nanomaterials.