q BIOL.689.01 - Rational Drug Design -- Bioinformatics
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BIOL.689.01 - Rational Drug Design -- Bioinformatics
Online Course, Spring 2017
Herbert J. Bernstein ()
Syllabus

  
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Welcome

Welcome to the syllabus web page for BIOL.689.01 - Rational Drug Design -- Bioinformatics, an online course at Rochester Institute of Technology, for Spring 2017. This is a 3 credit-hour graduate course for graduate students and open to upper level undergraduate students. The identification of the undergraduate section is BIOL.477.01. The course content is the same as for the graduate section.

Course Description

This course for graduate advanced undergraduate chemistry, biochemistry and bioinformatics students introduces the macromolecular-target computational-biology/bioinformatics aspects of rational drug design. This course is self-contained and complementary to CHEM.789.03 Rational Drug Design Cheminformatics which is oriented towards the small-molecule-ligand-oriented in silico physical chemistry aspects of Rational Drug Design. Topics include representation of macromolecular sequence and structural information, macromolecular databases and data mining, macromolecular drawing and interactive visualization, biological pathways, proteomics and metabolomics in drug design, structure-based drug design tools, design of ligands to fit macromolecular active sites, screening and assessing bind energies and affinities.

(Prerequisite: CHMB-403 or graduate standing in chemistry, biochemistry or bioinformatics or permission or the instructor)

Class 3, Credit 3 (S)

Instructor

What you will do in this course

This is a graduate level bioinformatics course open to advanced undergraduates as well as to graduate students. The primary goal for this course is for students to achieve an understanding of computational tools used to design drugs to interact with known macromolecular targets. A secondary goal is to develop or strengthen skills in working with computational chemistry and bioinformatics applications and databases. To achieve these goals you will study books and literature to understand the process of rational drug design or discovery of a ligand able to bind to a macromolecular active site, and will also work on a term project to gain and/or build on existing skills in using computer-aided drug design tools involving macromolecules. You will install software on your own computer and make use of programs already on remotely accessible computers. You will use a variety of databases on macromolecular structure and sequence, and on biological pathways. You will use some of the available molecular graphics programs and docking programs. There will be no midterm exam. You will be evaluated on the basis of assignments and reports at the midterm. At the end of the semester, you will be evaluated on a combination of assignments, reports, your term project and a final examination.

Resources

In addition to the current literature, you may find the following useful:

  1. Ghosh, Arun K., and Sandra Gemma. Structure-based Design of Drugs and Other Bioactive Molecules: Tools and Strategies. John Wiley & Sons, 2014.
  2. Larson, Richard S. (ed), Bioinformatics and Drug Discovery (Methods in Molecular Biology) 2nd ed. 2012 Edition, Humana Press; 2nd ed. 2012 edition (July 21, 2012)
  3. MacCuish, John David, and Norah E. MacCuish. Clustering in bioinformatics and drug discovery. CRC Press, 2010.
  4. http://click2drug.org (Swiss Institute of Bioinfomatics directory of computer aided drug design tools.

As of this writing, there is no single, suitable text book for this course. Instead we will draw on the current literature as primary sources.

You will also need a computer with a good internet connection and a web cam. On that computer, you should have (or get) a web browser. Further instructions for software to download will follow during the semester on the assignments page.

Course Outline

  1. Overview of Rational Drug Design, Ligands and Targets
  2. Representation of macromolecular sequence and structural information
    1. PDB Protein Data Bank format
    2. mmCIF IUCr Macromolecular Crystallographic Information File
    3. FASTA sequence format
    4. EMBL sequence format
    5. GenBank sequence format
    6. SwissProt sequence format
    7. PIR sequence format
    8. Other structure and sequence formats
  3. Macromolecular databases and data mining
    1. Protein Data Bank
    2. EMBL, GenBank, SwissProt sequence databases
    3. Other macromolecular databases
  4. Macromolecular drawing and interactive visualization Chimera, RasMol, PyMOL
  5. Biological pathways, proteomics and metabolomics in drug design Identifying targets
  6. Structure-based drug design tools
    1. Accuracy of macromolecular structural data
    2. Approximations used in modeling macromolecular target sites
    3. Design of ligands to fit macromolecular active sites
    4. Use of known ligands of homologs of the target
    5. Screening and assessing binding energies and affinities
    6. AutoDock and PyRx