title: Chemoinformatics in the New Era: From Molecular Dynamics to Systems Dynamics.
abstract: Chemoinformatics, due to its power in gathering information at the molecular level, has a wide array of important applications to biology, including fundamental biochemical studies and drug discovery and optimization. As modern "omics" based profiling and network based modeling and simulation techniques grow in sophistication, chemoinformatics now faces a great opportunity to include systems-level control mechanisms as one of its pillar components to extend and refine its various applications. This viewpoint article, through the example of computer aided targeting of the PI3K/Akt/mTOR pathway, outlines major steps of integrating systems dynamics simulations into molecular dynamics simulations to facilitate a higher level of chemoinformatics that would revolutionize drug lead optimization, personalized therapy, and possibly other applications.
authors.affiliation: Department of Biology, South University of Science and Technology of China, 1088 Xueyuan Rd., Shenzhen 518055, China. wanggy@sustc.edu.cn.
authors.forename: Guanyu
authors.initials: G
authors.lastname: Wang
mesh_terms: D019295:Computational Biology; D015195:Drug Design; D055808:Drug Discovery; D015870:Gene Expression; D006801:Humans; D056004:Molecular Dynamics Simulation; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics; D000081082:Phosphoinositide-3 Kinase Inhibitors; D057285:Precision Medicine; D047428:Protein Kinase Inhibitors / Q000138:chemical synthesis / Q000737:chemistry*; D051057:Proto-Oncogene Proteins c-akt / Q000037:antagonists & inhibitors* / Q000235:genetics; D021281:Quantitative Structure-Activity Relationship; D054852:Small Molecule Libraries; D058570:TOR Serine-Threonine Kinases / Q000037:antagonists & inhibitors* / Q000235:genetics; D014584:User-Computer Interface
chemical_list: D019869:Phosphatidylinositol 3-Kinases; D000081082:Phosphoinositide-3 Kinase Inhibitors; D047428:Protein Kinase Inhibitors; D051057:Proto-Oncogene Proteins c-akt; D054852:Small Molecule Libraries; D058570:TOR Serine-Threonine Kinases; C546842:MTOR protein, human
keywords: chemoinformatics; drug lead optimization; molecular dynamics simulation; systems dynamics simulation