LinkProt: A database of proteins with topological links

Input and output information

For more details on input and output information see:

Server - Analyze structuture

For detailed information on the results see Interpreting link data.

Single or two chains input: pdb file format

Standard file format from pdb database or custom pdb file. Server uses only Cα atoms. Define chain index or indices in submit form and loop ranges. It is possible to send bzip2-compressed file (with extension *.pdb.bz2).

Example of pdb file format

[...]
ATOM     24  CA  GLU A  24      14.212  33.180   1.863  1.00 64.63           C
ATOM     25  CA  GLU A  25      16.086  31.678  -1.097  1.00 59.03           C
ATOM     26  CA  GLU A  26      15.156  34.903  -2.877  1.00 41.85           C
ATOM     27  CA  GLY A  27      17.541  36.952  -0.744  1.00 46.12           C
ATOM     28  CA  VAL A  28      15.113  37.849   2.017  1.00 38.98           C
ATOM     29  CA  GLU A  29      16.989  38.371   5.242  1.00 43.20           C
ATOM     30  CA  TRP A  30      15.083  39.568   8.265  1.00 23.42           C
ATOM     31  CA  GLY A  31      16.419  41.023  11.489  1.00 19.92           C
ATOM     32  CA  TYR A  32      16.084  43.613  14.220  1.00 20.17           C
ATOM     33  CA  GLU A  33      18.064  46.492  12.735  1.00 20.57           C
[...]

Single chain input: xyz file format

A simple format which only contains atom numbers along the chain (in the first column) and Cartesian coordinates of all atoms in a chain (in second, third and fourth column); such a file cannot contain any additional columns. This format is suitable for analysis of chains other than proteins. It is possible to send bzip2-compressed file (with extension *.xyz.bz2).

Example of xyz file format

1       65.749        -49.197          15.303
2       69.453        -49.413          16.193
3       71.017        -51.127          19.196
4       72.074        -54.316          20.982
5       70.209        -57.190          22.570
6       70.849        -60.560          24.165
7       69.045        -63.421          22.445
8       68.973        -66.376          24.884
9       67.367        -68.701          22.324
[...]

Two chains input: xyz file format

Two files given in a simple format which only contains atom numbers along the chain (in the first column) and Cartesian coordinates of all atoms in a chain (in second, third and fourth column); such a file cannot contain any additional columns. Each file defines one chain. It is possible to send bzip2-compressed file (with extension *.xyz.bz2).

Example of xyz file format

1       65.749        -49.197          15.303
2       69.453        -49.413          16.193
3       71.017        -51.127          19.196
4       72.074        -54.316          20.982
5       70.209        -57.190          22.570
6       70.849        -60.560          24.165
7       69.045        -63.421          22.445
8       68.973        -66.376          24.884
9       67.367        -68.701          22.324
[...]

Currently accepts deterministically closed chains in xyz or pdb format.

Project name:

Email:

Input data format:

Select datafile in file format:

... or provide pdb code to download:

Whole chains:

Use whole chains (without specifying loop begins and ends)

Loops list:

Loop 1

chain:

begin:

end:

Loop 2

chain:

begin:

end:

Define first and last index of residue for loop closing.