Syllabus

From I571_2006_Wiki

The following topics will be covered in this course. For what is taught when, see the Schedule which will be developed over the course.

  • Introduction to the world of chemical informatics. Overview of the class; defining chemical informatics; chemical and bioinformatics; chemical informatics and the pharmaceutical industry; example applications; a glimpse of the future of chemical informatics
  • Representing 2D structures I. Kinds of 2D structure representation; atom lookup and connection tables; graph theory; SMILES; SD files; representation nuances; descriptors
  • Representing 2D structures II. Canonicalizing SMILES; representing reactions; representing generic structures; fingerprints; measuring chemical similarity; XML, CML, InChI and other web-oriented representation systems
  • 2D chemical database applications. Types of searching; substructure searching with SMARTS; similarity searching with fingerprints; demonstrations of searching systems
  • Advanced 2D descriptors. Kinds of descriptor; “mathematical” and topological indices; biological descriptors and their application in ADME/Tox; biological properties; property prediction software
  • Advanced 2D methods. 2D QSAR; cluster analysis; diversity analysis
  • Representing 3D structures. Sources of 3D information; experimental 3D databases; conformational flexibility; distance matrices; estimation of 3D structure; conformational search and minimization; 3D descriptors and fingerprint; representation of proteins
  • 3D visualization & computation. History of 3D visualization; free visualization and computation tools; 3D QSAR and models of activity; docking & virtual screening
  • Chemical informatics, bioinformatics, genomics and proteomics. The developing relationship between these fields
  • Practical high throughput screening analysis. A walkthrough of high throughput screening data analysisPractical molecular modeling
  • A walkthrough of the application of molecular modeling in drug design
  • Hot topics in the Pharmaceutical Industry. A discussion of current hot topics, including the intelligent use of large volumes of chemical and related information
  • Laboratory information management systems. Workflows in the laboratory; LIMS and SDMS architectures
  • Laboratory information management systems II. Current state of the art and issues
  • Commercial vendors & databases I. Systems for browsing databases (STN, SciFinder Scholar, Crossfire Commander); Commercial databases available (CAS, Beilstein, Cambridge Structural Dataset); Spectral Databases; Open Access issues
  • Commercial vendors & databases II. Product demonstrations
  • Electronic laboratory notebooks. Kinds of E-lab notebooks; authentication issues; adoption in the pharmaceutical industry; e-lab notebook functionality
  • Chemical & material science informatics in the process chemical industry. Characteristics of the industry; software development approaches; architectures
  • Chemical informatics software development I. Languages and programming toolkits; client/server software and web-based interfaces; the semantic web
  • Chemical informatics software development II. High performance computing; designing software for scientists
  • Chemical informatics software development III
  • Computational theoretical chemistry
  • Molecular mechanics and quantum mechanics
  • Computational models for ADME/Tox. The application of predictive models to pharmacology and toxicity testing (Dr. Sean Ekins, GeneGo)
  • Research overview and Literature Review. An overview of the state of the art in chemical informatics research
  • Panel Discussion. A chance to discuss current chemical informatics topics with industry and academia experts
  • Generic structures and searching. A detailed study of the representation and use of generic structures for patent and combinatorial chemistry applications
  • Emerging web service technologies for chemical informatics. A detailed look at how recent web developments such as the Semantic Web, web services, XML and RSS are likely to impact chemical informatics
  • Artificial Intelligence in chemical informatics. Foundations of AI; neural networks; recursive partitioning; support vector machines; genetic algorithms; intelligent agents
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