BCB697: Intruduction to Computational Structural Biology

Instructor: Dr. Wu

Assignments
Homework assignment 1
Problem 1 -->Display file:1HMV_pdb.htm; Downloadable file:1HMV.pdb
Problem 2 -->Description for the ATOM record
Problem 3 -->Picture 1, Picture 2, Picture 3
Homework assignment 2
Problem 1,2,3 -->Homework2
Second thoughts -->Seconds thoughts about homework2
Homework assignment 3
.m files -->With converge strategy:gradMethod.mWithout converge strategy:gradMetNoConv.m
Converge design and test results -->Converge design and testing results
Other functions -->The original function:fun1.mThe first derivative:grad1.m
Homework assignment 4
problem 1:--> Angle(ijkl)= 1.3198 Angle(jklm)=3.1220 command diary 1
problem 2:--> Angle(ijkl)= 1.3198 Angle(jklm)=3.1220 command diary 2
problem 3:--> dil= 3.0219 djm=3.7816 command diary 3
problem 4:--> xl=[34.0991,75.5695,225.6747] xm=[32.2546,75.7182,225.8504] command diary 4
Projects
Project 1
Readme file --> readme.doc
Problem 1 -->
Matlab program: extractCoord.m
Test file:1HMV.pdb
Test output file:1HMVcoords.dat
Problem 2 -->
Matlab program: update.m
Test file:1HMV.pdb 1HMVcoords.dat
Test output file:1HMV.pdb
Problem 3 -->
Matlab program: DME.m compDME.m
Test file:X.dat Y.dat
Problem 4 -->
Matlab program: RMSD.m compRMSD.m
Test file:X.dat Y.dat
Problem 5 -->
Protein structure files:1HMVp66original.pdb 1HMVp66computed.pdb
Coordinates file generated:p66ori.dat p66comp.dat
RMSD result:p66RMSD.doc
Project 2
Readme file --> Readme
Diary file --> Diary
Extract coordinates & generate distances -->
Matlab program: calcDis.m
Output file:x100.dat d100.dat
Calculate the coordinates from sparse distance -->
Main programfromSparseDtoC.m
Subfunctions:findBase.m find5thCoords.m atSamePlane.m
Output file:y100.dat
RMSD file:RMSD.m RMSD value is: 3.6161e-007
Create pdb file use newly generated coordinates -->
Matlab program: pdbFileCreator.m
Output file:1HMV_100atoms.pdb 1HMV_100atoms.GIF
Project 3
Readme file --> Readme
minEnergy --> MinEnergies
matlab files -->
multirun.m ljfun.m
simulatedAnnealing.m RMFileCreator.m
minimum energy configuration -->
5 clusters: coordinates minEnergy pdbFile RasMol
6 clusters: coordinates minEnergy pdbFile RasMol
7 clusters: coordinates minEnergy pdbFile RasMol
8 clusters: coordinates minEnergy pdbFile RasMol
9 clusters: coordinates minEnergy pdbFile RasMol
10 clusters: coordinates minEnergy pdbFile RasMol
11 clusters: coordinates minEnergy pdbFile RasMol
12 clusters: coordinates minEnergy pdbFile RasMol
13 clusters: coordinates minEnergy pdbFile RasMol
14 clusters: coordinates minEnergy pdbFile RasMol
15 clusters: coordinates minEnergy pdbFile RasMol
16 clusters: coordinates minEnergy pdbFile RasMol
17 clusters: coordinates minEnergy pdbFile RasMol
18 clusters: coordinates minEnergy pdbFile RasMol
19 clusters: coordinates minEnergy pdbFile RasMol
20 clusters: coordinates minEnergy pdbFile RasMol
21 clusters: coordinates minEnergy pdbFile RasMol
22 clusters: coordinates minEnergy pdbFile RasMol
23 clusters: coordinates minEnergy pdbFile RasMol
24 clusters: coordinates minEnergy pdbFile RasMol