Welcome to the syllabus web page for CHEM.789.03 - Rational Drug Design -- Cheminformatics, 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 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 small-molecule-ligand-oriented in silico physical chemistry aspects of rational drug
design. This course introduces the small-molecule-ligand-oriented in silico physical chemistry
aspects of rational drug design. Topics include in silico representation of chemical information,
chemical databases and data mining, molecular drawing and interactive visualization, computer-aided
drug design tools, building a ligand ab initio or from similar ligands, with and without known
macromolecules, assessing activity and toxicity and druggability.
(Prerequisite: CHMB-402 or graduate standing in chemistry, biochemistry or bioinformatics or
permission or the instructor)
Class 3, Credit 3 (S)
Instructor
Name: Herbert J. Bernstein
Position: Research Professor, School of Chemistry and Material Science
Office: Brookhaven National Laboratory, NSLS-II, Bldg 745, C08O, +1-631-344-8168
Contact Information: 5 Brewster Lane, Bellport, NY 11713
Office Hours: Because BNL is a seven hour drive from Rochester
it is impractical to meet in person,
so we will meet online via Skype (yayahjb) or Google Hangouts . See the scheduling information at
http://www.bernstein-plus-sons.com/.rit/HJB_Contact_Info.html
What you will do in this course
This is a graduate level cheminformatics 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
the in silico tools and techniques used to analyze and synthesize small molecule ligands to be
used as drugs acting on macromolecules. A secondary goal is to develop or strengthen skills in
working with computational chemistry and bioinformatics applications and databases.
In parallel with reading texts and online resources, you will be assigned important papers on
rational drug design to study and report on. You will have a drug design project to do to demonstrate your ability to design a druggable ligand
using computer-aided drug design tools.
Even though this is an on-line course, you will have regular e-meetings with the instructor and
classmates, 8 -- 9 pm Tuesday evenings .
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
The required text for this course is
Muthukumarasamy Karthikeyan and Renu Vyas. Practical chemoinformatics. Springer, 2014, soft-cover
ISBN 9788132234913
Things are changing rapidly, so we will also make extensive use of
on-line resources and the current literature.
In addition to the text, on-line resources and the current literature, you
may find the
following useful:
Silverman, Richard B., and Mark W. Holladay. The organic chemistry of drug design and drug
action. Academic press, 2014.
Bajorath, Jurgen. Chemoinformatics for Drug Discovery. John Wiley
& Sons, 2013.
http://click2drug.org (Swiss Institute of Bioinfomatics
directory of computer aided drug design
tools.
In addition to the text 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.
