2006 Spring Course Syllabus: AMS-536

Molecular Modeling of Biological Molecules

 
Spring 2006
Instructor: Dr. Robert C. Rizzo [631-632-9340, rizzo@ams.sunysb.edu]
Course: AMS-536 (3 Credits / 0 Audit) http://www.ams.sunysb.edu/~rizzo (go to Teaching)
When:   11:20AM-12:40PM, Monday and Wednesday, Math S235 (SINC site)
Office Hours:   Anytime or by appointment, Room 1-101, Dept. of Applied Math & Statistics
 
Hyperlinks accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.

 

Dates for Class Presentations
Speakers
02/20/2006

Jun Yong Choi
Roberto Colson

02/22/2006

Yan Yu (introduction to galaxy)
Amber Carr

02/27/2006

AJ Cambell
Li Cui

03/01/2006

Fangyu Ding
Raphael Geney

03/06/2006

Xingtao Liu
Matt Engel

03/08/2006

Fanling Meng
Mark Verdecia

03/13/2006

Jing Zhou
Noel Carrascal

03/15/2006 Jun Yong Choi
Roberto Colson
03/20/2006 Amber Carr
AJ Cambell
03/22/2006

Li Cui
Fangyu Ding

03/27/2006 Raphael Geney
Xingtao Liu
03/29/2006 Matt Engel
Fanling Meng
04/03/2006 Mark Verdecia
Jing Zhou
04/05/2006 Noel Carrascal
Jun Yong Choi
04/17/2006 Roberto Colson
Amber Carr
04/19/2006 AJ Cambell
Li Cui
04/24/2006 Fangyu Ding
Raphael Geney
04/26/2006 Xingtao Liu
Matt Engel
05/01/2006 Fanling Meng
Mark Verdecia
05/03/2006 Jing Zhou
Noel Carrascal
   
Final Project Notes
Files and Links
Project Guidelines
project.guidelines.pdf
Sample report project.example.dGhyd.pdf

Sample report

project.example.MMPS.pdf
Tutorials

 

Molecular Mechanics Tutorial Colby College Molecular Mechanics Tutorial
MOE program Tutorial Colby College MOE Tutorial
BOSS Owners Manual boss46.pdf
Amber8 Tutorial AMBER8_intro.pdf
Unix Tutorial for Beginners http://www.ee.surrey.ac.uk/Teaching/Unix
Vi Text Editor Tutorial At linux prompt type "vimtutor" (without the quotes)
Software
 
AMBER http://amber.scripps.edu/
BOSS / MCPRO http://zarbi.chem.yale.edu/
DOCK http://dock.compbio.ucsf.edu/
MOE (Chemical Computing Group) http://www.chemcomp.com/
VMD (visualization software) http://www.ks.uiuc.edu/Research/vmd/
Databases
 
NCI (ligand database) http://129.43.27.140/ncidb2/
NIST (small molecule database) http://webbook.nist.gov/chemistry/
ZINC (ligand database) http://blaster.docking.org/zinc/
   
If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact Disability Support Services (631) 632-6748.  They will determine with you what accommodations are necessary and appropriate.  All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and Disability Support Services.  For procedures and information go to the following website: http://www.ehs.sunysb.edu and search Fire Safety and Evacuation and Disabilities.