Biocomputing in Drug Design II
CHEM/CS 4003

Ghislain Deslongchamps, Department of Chemistry, U.N.B.
Rod Cooper, Faculty of Computer Science, U.N.B
Winter 2013

Calendar Description | Instructors | Timetable | Prerequisites | Enrollment | Textbook | D2L | Seminar | Examinations | Grading | Course Topics | Plagiarism

Calendar Description:

4ch (3C, 2L) follow-up of CHEM/CS 3003. Topics include pharmacophore perception, solvation models, free-energy calculations, multivariate statistics, genetic algorithms, principal component analysis, virtual drug libraries, chemical diversity and cheminformatics. Course includes lectures and computer laboratory component. Note: This course is cross-listed as CS 4003.


Ghislain Deslongchamps
Office: Toole 237
Phone: 453-4795
Rodney Cooper
Office: Gillin C107
Phone: 451-6964


January 7 - April 10, 2013


Prerequisite: CHEM/CS 3003.


12 students (priority will be given to graduating students)

Textbook (Optional):

Optional reference textbooks:


All lectures, courseware, and other materials developed for CHEM/CS 4003 is available through the D2L learning management system (, UNB PIN required).


- Each student will prepare and present one seminar near the end of the term. Seminars will be of a 20 minute duration, followed by a 5-10 minute question period (instructors and students). Topics must be on a recent research paper (2012-13) or review article related to computer-assisted drug design. All topics must be approved by either instructor by Monday, March 11. Scheduling will be determined on a first-come, first-serve basis. Seminar attendance is mandatory (5/100 mark penalty for any unjustified absence).
- Here is a sample list of appropriate journals for seminar preparation:
           Chemistry & Biology
           European Journal of Medicinal Chemistry

           Journal of Chemical Information and Modeling
           Journal of Computational Chemistry
           Journal of Computer-Aided Molecular Design
           Journal of The American Chemical Society
           Journal of Medicinal Chemistry
           Journal of Molecular Modeling
           Proceedings of the National Academy of Science

- Student seminars will be presented tentatively during the period of April 5-10.
- Course instructors will assign seminar grades based on Content (40%), Presentation (40%) and Handling of Questions (20%). Seminar presentations shorter than 15 min. will be penalized (-20%).

- Seminar report: Each student will prepare and submit a written report on the seminar topic based largely on the research paper presented. The report should be at least 5 double-spaced pages (excluding cover page, figures, and bibliography). All reports are due by April 10, 5pm. Late submissions will not be accepted.


- Friday afternoon lab attendance and full participation is mandatory. (5/100 mark penalty for any unjustified absence).
- Seminar attendance is mandatory (5/100 mark penalty for any unjustified absence).


Midterm* (in-class), Feb. 15, 2013: 30%
Seminar (in-class) April 5-10, 2013: 20%
Seminar report (due 5pm, April 10): 10%
Final exam* (TBA, Registrar's Office): 40%
TOTAL 100%

* closed-book examinations. Maple and MOE allowed.


90 %
85 %
80 %
74 %
68 %
62 %
56 %
50 %
40 %
<40 %

Course Topics (tentative listing):

Plagiarism (from 2012-2013 Undergraduate Calendar)

The University of New Brunswick places a high value on academic integrity and has a policy on plagiarism, cheating and other academic offences.

Plagiarism includes:
1. quoting verbatim or almost verbatim from any source, including all electronic sources, without acknowledgement;
2. adopting someone else’s line of thought, argument, arrangement, or supporting evidence without acknowledgement;
3. submitting someone else’s work, in whatever form without acknowledgement;
4. knowingly representing as one’s own work any idea of another.

Examples of other academic offences include: cheating on exams, tests, assignments or reports; impersonating somebody at a test or exam; obtaining an exam, test or other course materials through theft, collusion, purchase or other improper manner, submitting course work that is identical or substantially similar to work that has been submitted fro another course; and more as set out in the academic regulations found in the Undergraduate Calendar.

Penalties for plagiarism and other academic offences range from a minimum of F (zero) in the assignment, exam or test to a maximum of suspension or expulsion from the University, plus a notation of the academic offence on the student’s transcript.

For more information, please see the Undergraduate Regulation VIII, or visit It is the student’s responsibility to know the regulations.