Protein structure database (2017/11/30)

1130 Protein structure database 

課程重點

1.          Protein tool ExPASy

2.          Protein structure database

3.          Structure visualization tool PyMol

4.          Homology modeling

要做的練習

1.          BLAST : proteomic blast

2.          計算PI以及MW : proteomics – function analysis

3.          Protein sequence alignment : proteomics – ClustalW (NS1 file)

4.          Protein similarity search : proteomics FASRR/SSERACH/

5.          Prediction of secondary structure : proteomics-protein strictire-PROF

6.          Modeling of homologous structure : proteomics-protein strcture-SW

BLAST (BLAST target 1)

計算PI以及MW : proteomics – function analysis

Function analysis – Compute pI/MW • theoretical pI and Mw computation 

Protein sequence alignment : proteomics – ClustalW (NS1 file)

Protein data bank

Search: 3F8N

PDB上顯示的二級結構

Download protein sequence :

下載FASTA以及PDB

然後用Prediction of secondary structure : proteomics-protein strictire-PROF來預測3F8N

然後用PyMOL來做二級結構預測

背景變成白色 : display -> white

球的scale設定 : set sphere_scale = 0.4

叫出序列 , 選ZN , 將顏色設定成grays

選四個residue選起來 , selective 處 show side chain

將背景非目標物調淡 : Setting -> Tranparency -> cartoon -> 60%

叫出四個residue的label , selective  L (label) -> residues

設定label大小與顏色 :

Set label_color, black

Set label_size, -0.5

Wizard -> measurement -> distance -> 點選兩目標物及出現兩者間距離

將measure01-04顏色調整