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      QSAR without borders

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          Abstract

          Word cloud summary of diverse topics associated with QSAR modeling that are discussed in this review.

          Abstract

          Prediction of chemical bioactivity and physical properties has been one of the most important applications of statistical and more recently, machine learning and artificial intelligence methods in chemical sciences. This field of research, broadly known as quantitative structure–activity relationships (QSAR) modeling, has developed many important algorithms and has found a broad range of applications in physical organic and medicinal chemistry in the past 55+ years. This Perspective summarizes recent technological advances in QSAR modeling but it also highlights the applicability of algorithms, modeling methods, and validation practices developed in QSAR to a wide range of research areas outside of traditional QSAR boundaries including synthesis planning, nanotechnology, materials science, biomaterials, and clinical informatics. As modern research methods generate rapidly increasing amounts of data, the knowledge of robust data-driven modelling methods professed within the QSAR field can become essential for scientists working both within and outside of chemical research. We hope that this contribution highlighting the generalizable components of QSAR modeling will serve to address this challenge.

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          Most cited references244

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          Machine learning for molecular and materials science

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            Adverse outcome pathways: a conceptual framework to support ecotoxicology research and risk assessment.

            Ecological risk assessors face increasing demands to assess more chemicals, with greater speed and accuracy, and to do so using fewer resources and experimental animals. New approaches in biological and computational sciences may be able to generate mechanistic information that could help in meeting these challenges. However, to use mechanistic data to support chemical assessments, there is a need for effective translation of this information into endpoints meaningful to ecological risk-effects on survival, development, and reproduction in individual organisms and, by extension, impacts on populations. Here we discuss a framework designed for this purpose, the adverse outcome pathway (AOP). An AOP is a conceptual construct that portrays existing knowledge concerning the linkage between a direct molecular initiating event and an adverse outcome at a biological level of organization relevant to risk assessment. The practical utility of AOPs for ecological risk assessment of chemicals is illustrated using five case examples. The examples demonstrate how the AOP concept can focus toxicity testing in terms of species and endpoint selection, enhance across-chemical extrapolation, and support prediction of mixture effects. The examples also show how AOPs facilitate use of molecular or biochemical endpoints (sometimes referred to as biomarkers) for forecasting chemical impacts on individuals and populations. In the concluding sections of the paper, we discuss how AOPs can help to guide research that supports chemical risk assessments and advocate for the incorporation of this approach into a broader systems biology framework.
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              SchNet – A deep learning architecture for molecules and materials

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                Author and article information

                Journal
                CSRVBR
                Chemical Society Reviews
                Chem. Soc. Rev.
                Royal Society of Chemistry (RSC)
                0306-0012
                1460-4744
                June 8 2020
                2020
                : 49
                : 11
                : 3525-3564
                Affiliations
                [1 ]UNC Eshelman School of Pharmacy
                [2 ]University of North Carolina
                [3 ]Chapel Hill
                [4 ]USA
                [5 ]Department of Pharmaceutical Sciences
                [6 ]Department of Life Science Informatics
                [7 ]University of Bonn
                [8 ]Bonn
                [9 ]Germany
                [10 ]Merck & Co. Inc.
                [11 ]Kenilworth
                [12 ]Institute of Structural Biology
                [13 ]Helmholtz Zentrum München – Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) and BIGCHEM GmbH
                [14 ]Neuherberg
                [15 ]Institute of Biomedical Chemistry
                [16 ]Moscow
                [17 ]Russia
                [18 ]Department of Internal Medicine and UNM Comprehensive Cancer Center
                [19 ]University of New Mexico
                [20 ]Albuquerque
                [21 ]Department of Rheumatology
                [22 ]Department of Chemistry
                [23 ]University of Strasbourg
                [24 ]Strasbourg
                [25 ]France
                [26 ]Faculty of Physics
                [27 ]University of Florida
                [28 ]Gainesville
                [29 ]Materials Science
                [30 ]Center for Autonomous Materials Design
                [31 ]Duke University
                [32 ]Durham
                [33 ]North Carolina State University
                [34 ]Raleigh
                [35 ]Institute of The Environment and Sustainability
                [36 ]University of California
                [37 ]Los Angeles
                [38 ]University of Toronto
                [39 ]Toronto
                [40 ]Canada
                [41 ]Monash Institute of Pharmaceutical Sciences
                [42 ]Monash University
                [43 ]Melbourne
                [44 ]Australia
                [45 ]La Trobe Institute for Molecular Science
                [46 ]Novartis Institutes for BioMedical Research (NIBR)
                [47 ]Cambridge
                [48 ]Vancouver Prostate Centre
                [49 ]University of British Columbia
                [50 ]Vancouver
                Article
                10.1039/D0CS00098A
                32356548
                704c595c-4810-4cd0-9ce6-29d766786ee5
                © 2020

                http://creativecommons.org/licenses/by-nc/3.0/

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