Step1 : Input Protein Sequence (Single letter Code)
For eg: 'PAAAASWVKSNIQAYPKVSFRYVCVGN '
Step 2: Input secondary Structure Information: Specify secondary structure information to give Helix or Sheet information(optional)
For eg you want Helix region from 1- 12 amino acid and Sheet from 12 - 27
Helix : 1-12
Sheet : 21-27
Step3 :Click on Customize dihedrals to get Dihedral information. If you want to change the dihedral information for an amino acid, you can do it by editing the corresponding value.
| 1 |
NPRO |
-58.00 -36.40 |
H |
| 2 |
ALA |
-63.60 -39.30 |
H |
| 3 |
ALA |
-63.60 -39.30 |
H |
| 4 |
ALA |
-63.60 -39.30 |
H |
| 5 |
ALA |
-63.60 -39.30 |
H |
| 6 |
SER |
-65.80 -36.50 |
H |
| 7 |
TRP |
-64.70 -40.10 |
H |
| 8 |
VAL |
-65.50 -41.70 |
H |
| 9 |
LYS |
-64.70 -39.40 |
H |
| 10 |
SER |
-65.80 -36.50 |
H |
| 11 |
ASN |
-66.60 -36.00 |
H |
| 12 |
ILE |
-65.10 -42.10 |
H |
| 13 |
GLN |
-105.00 125.00 |
L |
| 14 |
ALA |
-125.00 135.00 |
L |
| 15 |
TYR |
-125.00 145.00 |
L |
| 16 |
PRO |
-65.00 145.00 |
L |
| 17 |
LYS |
-85.00 -25.00 |
L |
| 18 |
VAL |
-125.00 145.00 |
L |
| 19 |
SER |
-75.00 145.00 |
L |
| 20 |
PHE |
-125.00 155.00 |
L |
| 21 |
ARG |
-110.00 150.00 |
S |
| 22 |
TYR |
-110.00 160.00 |
S |
| 23 |
VAL |
-110.00 150.00 |
S |
| 24 |
CYS |
-110.00 150.00 |
S |
| 25 |
VAL |
-110.00 150.00 |
S |
| 26 |
GLY |
160.00 180.00 |
S |
| 27 |
CASN |
-110.00 150.00 |
S |
Step 4: Enter pdb name: xyz (This wll generate PDB file by the file name provided by you)
Click on ‘Generate structure’ ,it will generate 'xyz.pdb'
xyz.pdb (PDB Format)
In case of biophysical filters(Persistence length, Radius of gyration, Packing fraction, Hydrophobicity) go to next Step i.e. 'Generated files'.
Check the box in front of xyz.pdb to select the structure.
Click on Filter to calculate the filter value for eg. If you are trying to filter on Persistence Length, the tabular output shows the name of the pdb file, the value of persistence
length and the length of the longest secondary structural element.
| PDB Name |
Value |
Max. Sec Str Length |
Filtered |
| xyz.pdb |
45.465873 |
12 |
 |
A tick mark () shows that the structure is selected (native-like) by the filter whereas a cross (X) indicates that the structure is rejected (non-native like).
|