PEPstrMOD: Peptide Tertiary Structure Prediction with Natural, Non-natural Modified Residues.

Welcome to Advance Modification Module with Manual Modification

This module provides an option to open any PDB structure in a web based chemical drawing software (Marvin Applet) and user can add any modification in any particular position on the structure and submit it. The submitted initial structure will be subjected to energy minimization by open babel software and minimized structure will be given as output. This service will be useful for incorporating modifications whose force field parameters are not present in the standard force field libraries used in this study. For more information click help
Suggestion: If a user wants to edit any structure in his/her own favorite editor/software (like Pymol etc), he/she can do it and open that structure here in marvin sketch and submit the structure here.

Peptide Structure Manual Modification using Marvin

4Q1L.pdb
 OpenBabel05191516483D

29 29  0  0  1  0  0  0  0  0999 V2000
    5.2500  -21.0240   18.6170 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9350  -21.0870   19.2450 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9400  -21.9060   18.4220 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3330  -22.6610   17.5220 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3690  -19.6790   19.4620 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1070  -18.9140   18.1830 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0730  -17.8260   18.3560 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4380  -16.7080   18.8010 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8940  -18.0960   18.0380 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6570  -21.7460   18.7590 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5270  -22.3190   18.0300 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6710  -22.1030   16.5280 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3240  -22.9750   15.7270 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7640  -21.6260   18.4730 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7430  -22.4580   19.2890 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9670  -21.6440   19.6800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9420  -20.4110   19.6180 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0440  -22.3240   20.0760 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1610  -20.9250   16.1530 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2880  -20.5790   14.7520 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7270  -20.3520   14.3870 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4640  -19.6380   15.0690 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4830  -19.3230   14.4150 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9940  -19.5080   14.5050 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6630  -19.2750   15.7000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7210  -19.9120   13.3950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0380  -19.4360   15.7830 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0870  -20.0760   13.4710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7470  -19.8380   14.6660 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  6  0  0  0
  2  5  1  0  0  0  0
  3 10  1  0  0  0  0
  4  3  2  0  0  0  0
  6  7  1  0  0  0  0
  6  5  1  0  0  0  0
  7  8  2  0  0  0  0
  9  7  1  0  0  0  0
 11 12  1  6  0  0  0
 11 14  1  0  0  0  0
 11 10  1  0  0  0  0
 13 12  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 18  1  0  0  0  0
 17 16  2  0  0  0  0
 19 12  1  0  0  0  0
 20 21  1  1  0  0  0
 20 19  1  0  0  0  0
 21 22  2  0  0  0  0
 23 24  1  0  0  0  0
 23 20  1  0  0  0  0
 24 25  2  0  0  0  0
 25 27  1  0  0  0  0
 26 28  2  0  0  0  0
 26 24  1  0  0  0  0
 28 29  1  0  0  0  0
 29 27  2  0  0  0  0
M  END
$$$$

Note: Chrome browser may have some compatibility issues with the above Marvin applet. This applet is best visualized in Firefox and Safari browsers.