Coms/Math/BCB 597

fall 2003

since 2003-08-27

Jie Bao

lab2 : distance geometry optimization
2003-10-27

The run file:  lab2.m
The distance geometry optimization file: dgfun.m   Reference: fminunc , optimset
The data file: data.dat x0.dat
The result: result.txt
 

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HW4 : Coordinates and Angles

the matlab file

HW3 : Newton Method

2003-10-01

See the page

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Lab 1: Computing DME and RSMD

 2003-09-26

Readme

 Please download the dataset first: 1HVM.pdb(unzip to protein.pdb), 1HMVp66original.pdb , 1HMVp66computed.pdb
 To run : download and unpack the m file package  to the same folder to  data files
 Result: result.txt

• Question1: Extract coordinates from PDB file
• Question2: Update coordinates in a PDB file
• Question3: Compute the DME(Distance Matrix Error) of two protein data
• Question4: Compute the RMSD(Root-Mean-Square Deviation) of two protein data

Homework 1: Get familiar with PDB database and RasMol

2003-09-05

• Problem1 -> 1HVM.pdb (zipped)
• Problem2 -> Description for the ATOM record  (PDB File Format)
• Problem3 [Software : Protein Explorer, Chime & RasMol (or http://openrasmol.org/ ) RasMol 2.7.2.1 ]
• Picture1 , (Display -> Stick,   Colors -> Group)
• Picture2 , (Display -> Space Filling,   Colors -> Chain)
• Picture3 , (Display -> Ribons,   Colors ->Structure)
• Extra Credit -> 20 Amino Acids