Literature DB >> 32663517

Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling.

Linlin Zhao1, Heather L Ciallella1, Lauren M Aleksunes2, Hao Zhu3.   

Abstract

Advancing a new drug to market requires substantial investments in time as well as financial resources. Crucial bioactivities for drug candidates, including their efficacy, pharmacokinetics (PK), and adverse effects, need to be investigated during drug development. With advancements in chemical synthesis and biological screening technologies over the past decade, a large amount of biological data points for millions of small molecules have been generated and are stored in various databases. These accumulated data, combined with new machine learning (ML) approaches, such as deep learning, have shown great potential to provide insights into relevant chemical structures to predict in vitro, in vivo, and clinical outcomes, thereby advancing drug discovery and development in the big data era.
Copyright © 2020 Elsevier Ltd. All rights reserved.

Entities:  

Year:  2020        PMID: 32663517      PMCID: PMC7572559          DOI: 10.1016/j.drudis.2020.07.005

Source DB:  PubMed          Journal:  Drug Discov Today        ISSN: 1359-6446            Impact factor:   7.851


  175 in total

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Authors:  Vivek Swarup; Daniel H Geschwind
Journal:  Nature       Date:  2013-07-24       Impact factor: 49.962

3.  Update of TTD: Therapeutic Target Database.

Authors:  Feng Zhu; BuCong Han; Pankaj Kumar; XiangHui Liu; XiaoHua Ma; Xiaona Wei; Lu Huang; YangFan Guo; LianYi Han; ChanJuan Zheng; YuZong Chen
Journal:  Nucleic Acids Res       Date:  2009-11-20       Impact factor: 16.971

Review 4.  Emerging applications of metabolomics in drug discovery and precision medicine.

Authors:  David S Wishart
Journal:  Nat Rev Drug Discov       Date:  2016-03-11       Impact factor: 84.694

5.  Evaluation of binary QSAR models derived from LUDI and MOE scoring functions for structure based virtual screening.

Authors:  Philip Prathipati; Anil K Saxena
Journal:  J Chem Inf Model       Date:  2006 Jan-Feb       Impact factor: 4.956

Review 6.  Advancing Computational Toxicology in the Big Data Era by Artificial Intelligence: Data-Driven and Mechanism-Driven Modeling for Chemical Toxicity.

Authors:  Heather L Ciallella; Hao Zhu
Journal:  Chem Res Toxicol       Date:  2019-03-25       Impact factor: 3.739

7.  Toward interoperable bioscience data.

Authors:  Susanna-Assunta Sansone; Philippe Rocca-Serra; Dawn Field; Eamonn Maguire; Chris Taylor; Oliver Hofmann; Hong Fang; Steffen Neumann; Weida Tong; Linda Amaral-Zettler; Kimberly Begley; Tim Booth; Lydie Bougueleret; Gully Burns; Brad Chapman; Tim Clark; Lee-Ann Coleman; Jay Copeland; Sudeshna Das; Antoine de Daruvar; Paula de Matos; Ian Dix; Scott Edmunds; Chris T Evelo; Mark J Forster; Pascale Gaudet; Jack Gilbert; Carole Goble; Julian L Griffin; Daniel Jacob; Jos Kleinjans; Lee Harland; Kenneth Haug; Henning Hermjakob; Shannan J Ho Sui; Alain Laederach; Shaoguang Liang; Stephen Marshall; Annette McGrath; Emily Merrill; Dorothy Reilly; Magali Roux; Caroline E Shamu; Catherine A Shang; Christoph Steinbeck; Anne Trefethen; Bryn Williams-Jones; Katherine Wolstencroft; Ioannis Xenarios; Winston Hide
Journal:  Nat Genet       Date:  2012-01-27       Impact factor: 38.330

8.  GCAC: galaxy workflow system for predictive model building for virtual screening.

Authors:  Deepak R Bharti; Anmol J Hemrom; Andrew M Lynn
Journal:  BMC Bioinformatics       Date:  2019-02-04       Impact factor: 3.169

9.  Mechanism Profiling of Hepatotoxicity Caused by Oxidative Stress Using Antioxidant Response Element Reporter Gene Assay Models and Big Data.

Authors:  Marlene Thai Kim; Ruili Huang; Alexander Sedykh; Wenyi Wang; Menghang Xia; Hao Zhu
Journal:  Environ Health Perspect       Date:  2015-09-18       Impact factor: 9.031

10.  PubChem 2019 update: improved access to chemical data.

Authors:  Sunghwan Kim; Jie Chen; Tiejun Cheng; Asta Gindulyte; Jia He; Siqian He; Qingliang Li; Benjamin A Shoemaker; Paul A Thiessen; Bo Yu; Leonid Zaslavsky; Jian Zhang; Evan E Bolton
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

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  16 in total

1.  The Brazilian compound library (BraCoLi) database: a repository of chemical and biological information for drug design.

Authors:  Gabriel Corrêa Veríssimo; Valtair Severino Dos Santos Júnior; Ingrid Ariela do Rosário de Almeida; Marina Sant'Anna Mitraud Ruas; Lukas Galuppo Coutinho; Renata Barbosa de Oliveira; Ricardo José Alves; Vinícius Gonçalves Maltarollo
Journal:  Mol Divers       Date:  2022-01-28       Impact factor: 2.943

2.  Automatic Quantitative Structure-Activity Relationship Modeling to Fill Data Gaps in High-Throughput Screening.

Authors:  Heather L Ciallella; Elena Chung; Daniel P Russo; Hao Zhu
Journal:  Methods Mol Biol       Date:  2022

Review 3.  Artificial intelligence and machine-learning approaches in structure and ligand-based discovery of drugs affecting central nervous system.

Authors:  Vertika Gautam; Anand Gaurav; Neeraj Masand; Vannajan Sanghiran Lee; Vaishali M Patil
Journal:  Mol Divers       Date:  2022-07-11       Impact factor: 3.364

Review 4.  Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process.

Authors:  Md Rifat Hasan; Ahad Amer Alsaiari; Burhan Zain Fakhurji; Mohammad Habibur Rahman Molla; Amer H Asseri; Md Afsar Ahmed Sumon; Moon Nyeo Park; Foysal Ahammad; Bonglee Kim
Journal:  Molecules       Date:  2022-06-29       Impact factor: 4.927

Review 5.  Prediction of antischistosomal small molecules using machine learning in the era of big data.

Authors:  Samuel K Kwofie; Kwasi Agyenkwa-Mawuli; Emmanuel Broni; Whelton A Miller Iii; Michael D Wilson
Journal:  Mol Divers       Date:  2021-08-05       Impact factor: 2.943

Review 6.  Alkaloids in Contemporary Drug Discovery to Meet Global Disease Needs.

Authors:  Sharna-Kay Daley; Geoffrey A Cordell
Journal:  Molecules       Date:  2021-06-22       Impact factor: 4.411

Review 7.  The Combination of Tradition and Future: Data-Driven Natural-Product-Based Treatments for Parkinson's Disease.

Authors:  Zhijun Miao; Jinwei Bai; Li Shen; Rajeev K Singla
Journal:  Evid Based Complement Alternat Med       Date:  2021-07-14       Impact factor: 2.629

8.  Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery.

Authors:  Manish Kumar Tripathi; Abhigyan Nath; Tej P Singh; A S Ethayathulla; Punit Kaur
Journal:  Mol Divers       Date:  2021-06-23       Impact factor: 3.364

Review 9.  Molecular Modeling Targeting Transmembrane Serine Protease 2 (TMPRSS2) as an Alternative Drug Target Against Coronaviruses.

Authors:  Igor José Dos Santos Nascimento; Edeildo Ferreira da Silva-Júnior; Thiago Mendonça de Aquino
Journal:  Curr Drug Targets       Date:  2022       Impact factor: 2.937

10.  Revealing Adverse Outcome Pathways from Public High-Throughput Screening Data to Evaluate New Toxicants by a Knowledge-Based Deep Neural Network Approach.

Authors:  Heather L Ciallella; Daniel P Russo; Lauren M Aleksunes; Fabian A Grimm; Hao Zhu
Journal:  Environ Sci Technol       Date:  2021-07-25       Impact factor: 11.357

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