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      Artificial intelligence and machine learning approaches for drug design: challenges and opportunities for the pharmaceutical industries

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          Abstract

          Abstract

          The global spread of COVID-19 has raised the importance of pharmaceutical drug development as intractable and hot research. Developing new drug molecules to overcome any disease is a costly and lengthy process, but the process continues uninterrupted. The critical point to consider the drug design is to use the available data resources and to find new and novel leads. Once the drug target is identified, several interdisciplinary areas work together with artificial intelligence (AI) and machine learning (ML) methods to get enriched drugs. These AI and ML methods are applied in every step of the computer-aided drug design, and integrating these AI and ML methods results in a high success rate of hit compounds. In addition, this AI and ML integration with high-dimension data and its powerful capacity have taken a step forward. Clinical trials output prediction through the AI/ML integrated models could further decrease the clinical trials cost by also improving the success rate. Through this review, we discuss the backend of AI and ML methods in supporting the computer-aided drug design, along with its challenge and opportunity for the pharmaceutical industry.

          Graphic abstract

          From the available information or data, the AI and ML based prediction for the high throughput virtual screening. After this integration of AI and ML, the success rate of hit identification has gained a momentum with huge success by providing novel drugs.

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          Most cited references184

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          Is Open Access

          SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules

          To be effective as a drug, a potent molecule must reach its target in the body in sufficient concentration, and stay there in a bioactive form long enough for the expected biologic events to occur. Drug development involves assessment of absorption, distribution, metabolism and excretion (ADME) increasingly earlier in the discovery process, at a stage when considered compounds are numerous but access to the physical samples is limited. In that context, computer models constitute valid alternatives to experiments. Here, we present the new SwissADME web tool that gives free access to a pool of fast yet robust predictive models for physicochemical properties, pharmacokinetics, drug-likeness and medicinal chemistry friendliness, among which in-house proficient methods such as the BOILED-Egg, iLOGP and Bioavailability Radar. Easy efficient input and interpretation are ensured thanks to a user-friendly interface through the login-free website http://www.swissadme.ch. Specialists, but also nonexpert in cheminformatics or computational chemistry can predict rapidly key parameters for a collection of molecules to support their drug discovery endeavours.
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            The Genotype-Tissue Expression (GTEx) project.

            Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions probably contribute to many disease phenotypes. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.
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              Is Open Access

              The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation

              Background To evaluate binary classifications and their confusion matrices, scientific researchers can employ several statistical rates, accordingly to the goal of the experiment they are investigating. Despite being a crucial issue in machine learning, no widespread consensus has been reached on a unified elective chosen measure yet. Accuracy and F1 score computed on confusion matrices have been (and still are) among the most popular adopted metrics in binary classification tasks. However, these statistical measures can dangerously show overoptimistic inflated results, especially on imbalanced datasets. Results The Matthews correlation coefficient (MCC), instead, is a more reliable statistical rate which produces a high score only if the prediction obtained good results in all of the four confusion matrix categories (true positives, false negatives, true negatives, and false positives), proportionally both to the size of positive elements and the size of negative elements in the dataset. Conclusions In this article, we show how MCC produces a more informative and truthful score in evaluating binary classifications than accuracy and F1 score, by first explaining the mathematical properties, and then the asset of MCC in six synthetic use cases and in a real genomics scenario. We believe that the Matthews correlation coefficient should be preferred to accuracy and F1 score in evaluating binary classification tasks by all scientific communities.
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                Author and article information

                Contributors
                selnikraj@bioclues.org
                skysanjeev@gmail.com
                Journal
                Mol Divers
                Mol Divers
                Molecular Diversity
                Springer International Publishing (Cham )
                1381-1991
                1573-501X
                23 October 2021
                : 1-21
                Affiliations
                GRID grid.411312.4, ISNI 0000 0001 0363 9238, CADD and Molecular Modelling Lab, Department of Bioinformatics, , Alagappa University, ; Science Block, Karaikudi, Tamil Nadu 630004 India
                Article
                10326
                10.1007/s11030-021-10326-z
                8536481
                34686947
                392a4da0-e0ee-463b-9f07-aa0d42b9226a
                © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2021

                This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

                History
                : 5 April 2021
                : 24 September 2021
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100008762, tamil nadu state council for higher education;
                Award ID: 117/2021
                Award ID: 117/2021
                Award Recipient :
                Categories
                Short Review

                Molecular biology
                artificial intelligence,machine learning,deep learning,pharmaceutical industry,imaging

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