Journal Article10.1016/J.DRUDIS.2010.04.003
Evolving molecules using multi-objective optimization: applying to ADME/Tox.
TL;DR: This work discusses how multi-objective optimization can be used for drug discovery, focusing on evolutionary molecule design to incorporate optimal predicted absorption, distribution, metabolism, excretion and toxicity properties in Pareto Ligand Designer.
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About: This article is published in Drug Discovery Today. The article was published on 01 Jun 2010. The article focuses on the topics: Multi-objective optimization & Pareto principle.
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Citations
Rethinking drug design in the artificial intelligence era
Petra Schneider,W. Patrick Walters,Alleyn T. Plowright,Norman Sieroka,Jennifer Listgarten,Robert Alan Goodnow,Jasmin Fisher,Jasmin Fisher,Johanna M. Jansen,José S. Duca,Thomas S. Rush,Matthias Zentgraf,John Edward Hill,Elizabeth Krutoholow,Matthias Kohler,Jeff Blaney,Kimito Funatsu,Kimito Funatsu,Chris Luebkemann,Chris Luebkemann,Gisbert Schneider +20 more
TL;DR: The views of a diverse group of international experts on the ‘grand challenges’ in small-molecule drug discovery with AI are presented, including obtaining appropriate data sets, generating new hypotheses, optimizing in a multi-objective manner, reducing cycle times and changing the research culture.
Discovery of small molecule cancer drugs: Successes, challenges and opportunities
TL;DR: This review provides an overview of contemporary approaches to the discovery of small molecule cancer drugs, highlighting successes, current challenges and future opportunities, and focuses in particular on four key steps: Target validation and selection; chemical hit and lead generation; lead optimization to identify a clinical drug candidate; and finally hypothesis‐driven, biomarker‐led clinical trials.
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Comparison of Deep Learning With Multiple Machine Learning Methods and Metrics Using Diverse Drug Discovery Data Sets.
TL;DR: The aim was to assess whether deep learning offered any improvement in testing when assessed using an array of metrics including AUC, F1 score, Cohen's kappa, Matthews correlation coefficient and others, and based on ranked normalized scores for the metrics or data sets Deep Neural Networks (DNN) ranked higher than SVM, which in turn wasranked higher than all the other machine learning methods.
336
Clustered patterns of species origins of nature-derived drugs and clues for future bioprospecting
Feng Zhu,Chu Qin,Lin Tao,Xin Liu,Zhe Shi,Xiao Hua Ma,Jia Jia,Ying Tan,Cheng Cui,Jin-Shun Lin,Chunyan Tan,Yuyang Jiang,Yu Zong Chen +12 more
TL;DR: Four lines of evidence from historical drug data, 13,548 marine natural products, 767 medicinal plants, and 19,721 bioactive natural products suggest that drugs are derived mostly from preexisting drug-productive families.
252
Multi-objective optimization methods in drug design.
TL;DR: This paper reviews the latest multi-objective methods and applications reported in the literature, specifically in quantitative structure–activity modeling, docking, de novo design and library design.
References
A fast and elitist multiobjective genetic algorithm: NSGA-II
TL;DR: This paper suggests a non-dominated sorting-based MOEA, called NSGA-II (Non-dominated Sorting Genetic Algorithm II), which alleviates all of the above three difficulties, and modify the definition of dominance in order to solve constrained multi-objective problems efficiently.
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
TL;DR: Experimental and computational approaches to estimate solubility and permeability in discovery and development settings are described in this article, where the rule of 5 is used to predict poor absorption or permeability when there are more than 5 H-bond donors, 10 Hbond acceptors, and the calculated Log P (CLogP) is greater than 5 (or MlogP > 415).
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A Fast Elitist Non-dominated Sorting Genetic Algorithm for Multi-objective Optimisation: NSGA-II
Kalyanmoy Deb,Samir Agrawal,Amrit Pratap,T. Meyarivan +3 more
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TL;DR: Simulation results on five difficult test problems show that the proposed NSGA-II, in most problems, is able to find much better spread of solutions and better convergence near the true Pareto-optimal front compared to PAES and SPEA--two other elitist multi-objective EAs which pay special attention towards creating a diverse Paretimal front.
Simultaneous Optimization of Several Response Variables
TL;DR: In this article, the authors present a set of conditions that will result in a product with a desirable combination of properties, which is a problem facing the product development community in general.
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The price of innovation: new estimates of drug development costs
TL;DR: The research and development costs of 68 randomly selected new drugs were obtained from a survey of 10 pharmaceutical firms and used to estimate the average pre-tax cost of new drug development.
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