Chulalongkorn University

Research and Education

Biomolecular Modeling

Time and Room: every Friday 10-12 (R1123) & 13.30-15.30 at Self-Learning Center (Department Library)

Course syllabus

Class schedule

Lecture notes

·  Chapter 1 : Introduction : Webminar movie

·  Chapter 1 : Introduction-2 : vmd tutorial

· Chapter 2: Biomolecules-1 : workshop III

· Chapter 2: Biomolecules-2 : workshop IV

· MD simulation  (Aj.TR)

· Chapter 5 :Virtual screening : workshop IX-A

· Chapter 6 :Protein structure prediction: workshop-handout : workshop IX-B  exercise 

· Chapter 7 :Molecular docking : workshop X

Examination

- Final : Student presentation (15 min/person + 5 min questions)

- Quiz: 10 minutes

Supplementary Materials

Articles, Assignment: Articles#1  Access PDB files and papers  

Scripts: color.tcl

Guidelines, instructions: : Vi-editor

Software

- VMD v1.9 for windows      - Pymol v0.99 for windows

- Rasmol v2.6                     - Editplus v3.11

- Putty                               - SSH

- APBS                               - ISIS Draw

- NAMD 2.8 for windows     - Autodock

- ADT tools                          - Autodock vina

- NX_Client_3.5                  - Qutemol

- LigPlot                              - Chemsketch

- Open babel

Download PDB files

 

Please often check my web for news, update or announcement of the class

 

Useful links

Theoretical Biophysics Group : www.ks.uiuc.edu/Research/vmd/

Protein Data Bank :  www.rcsb.org

Pubmed, Entrez, GenBank, Blast, PubChem: www.ncbi.nlm.nih.gov

FF Topology: www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/node4.html