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Computing side chain conformations by simulated annealing with frozen main chain atoms

GETATOMS is a program of modeling atomic coordinates of a protein with unknown 3D structure. It uses main chain coordinates from 3D structure of similar protein, which sequence is aligned with a query protein. Restoration of loops in alignment will be added later.
GETATOMS also has an option to provide coordinates of H-atoms.

GETATOMS computes 3D protein coordinates of a query protein and estimates quality of produced 3D structure using several scores:

  • Steric_Score similar to described in JMB (1997), 267, 1268-1282
  • VDW_Score similar to JMB(1981) v.153,p.1087-1109
  • Bump Score - a number of atomic pairs having sterically forbidden overlap.

Resulting 3D structure can be visualized using 3D-viewers such as RasMol.

INPUT is PDB structure of similar protein with known 3D structure and alignment of query sequence and template protein sequence in several formats.

For example, if we have 4hhb (A) sequence as query and 1hba(B) as template, simple format:

      VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDL------SHGSAQVKGHGKKVAD
      HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPRTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG

      ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVST
      AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN

      VLTSKYR
      ALAHKYH

GETATOMS output:

      HEADER    OXYGEN TRANSPORT                        07-MAR-84   4HHB    
      REMARK  50
      REMARK  50 GETATOMS [ver=0.9.0.0; date=20020312]
      REMARK  50 Modelled from template structure provided by user.
      REMARK  50 Calculation parameters:
      REMARK  50   Simulated Annealing Temperature=2.000000
      REMARK  50   Simulated Annealing Maximal number of steps=100
      REMARK  50   Simulated Annealing steps done=-1073216864
      REMARK  50   Add Hydrogen Atoms=OFF
      REMARK  50 Final score data:
      REMARK  50   VDW_Score=1.089206e-19
      REMARK  50   Steric_Score=2.652495e-315
      REMARK  50   Bump_Score=0.000000e+00
      ATOM      1  N   VAL     1       9.223 -20.614   1.365
      ATOM      2  CA  VAL     1       8.694 -20.026  -0.123
      ATOM      3  C   VAL     1       9.668 -21.068  -1.645
      ATOM      4  O   VAL     1       9.370 -22.612  -0.994
      ATOM      5  CB  VAL     1       8.948 -18.511  -0.251
      ATOM      6  CG1 VAL     1       8.554 -18.010  -1.636
      ATOM      7  CG2 VAL     1       8.176 -17.751   0.822
      ATOM      8  N   LEU     2       9.270 -20.650  -2.180
      ATOM      9  CA  LEU     2      10.245 -21.378  -3.143
      ATOM     10  C   LEU     2      11.419 -20.331  -4.099
      ATOM     11  O   LEU     2      11.252 -19.250  -5.024
      ATOM     12  CB  LEU     2       9.461 -22.198  -4.174
      ATOM     13  CG  LEU     2       8.651 -23.375  -3.627
      ATOM     14  CD1 LEU     2       7.843 -24.024  -4.741
      ATOM     15  CD2 LEU     2       9.576 -24.392  -2.976
      ATOM     16  N   SER     3      12.365 -20.722  -3.649
      ATOM     17  CA  SER     3      13.611 -20.183  -4.477
      ATOM     18  C   SER     3      14.557 -21.356  -5.125
      ATOM     19  O   SER     3      14.340 -22.536  -4.780
      ATOM     20  CB  SER     3      14.497 -19.299  -3.595
      ATOM     21  OG  SER     3      15.076 -20.068  -2.554

      or  WITH H-atoms:

      REMARK  50   Add Hydrogen Atoms=ON
      REMARK  50 Final score data:
      REMARK  50   VDW_Score=1.089206e-19
      REMARK  50   Steric_Score=2.652495e-315
      REMARK  50   Bump_Score=0.000000e+00
      ATOM      1  N   VAL     1       9.223 -20.614   1.365
      ATOM      2  CA  VAL     1       8.694 -20.026  -0.123
      ATOM      3  C   VAL     1       9.668 -21.068  -1.645
      ATOM      4  O   VAL     1       9.370 -22.612  -0.994
      ATOM      5  CB  VAL     1       8.948 -18.511  -0.251
      ATOM      6  CG1 VAL     1       8.554 -18.010  -1.636
      ATOM      7  CG2 VAL     1       8.176 -17.751   0.822
      ATOM      8 1H   VAL     1      10.102 -20.497   1.435
      ATOM      9 2H   VAL     1       8.812 -20.175   2.021
      ATOM     10 3H   VAL     1       9.034 -21.482   1.426
      ATOM     11  HA  VAL     1       9.166 -20.592  -0.926
      ATOM     12  HB  VAL     1      10.006 -18.305  -0.091
      ATOM     13 1HG1 VAL     1       9.071 -17.073  -1.845
      ATOM     14 2HG1 VAL     1       8.833 -18.752  -2.384
      ATOM     15 3HG1 VAL     1       7.477 -17.846  -1.671
      ATOM     16 1HG2 VAL     1       7.168 -17.540   0.463
      ATOM     17 2HG2 VAL     1       8.120 -18.356   1.727
      ATOM     18 3HG2 VAL     1       8.686 -16.814   1.043
      ATOM     19  N   LEU     2       9.270 -20.650  -2.180
      ATOM     20  CA  LEU     2      10.245 -21.378  -3.143
      ATOM     21  C   LEU     2      11.419 -20.331  -4.099
      ATOM     22  O   LEU     2      11.252 -19.250  -5.024
      ATOM     23  CB  LEU     2       9.461 -22.198  -4.174
      ATOM     24  CG  LEU     2       8.651 -23.375  -3.627
      ATOM     25  CD1 LEU     2       7.843 -24.024  -4.741
      ATOM     26  CD2 LEU     2       9.576 -24.392  -2.976
      ATOM     27  H   LEU     2       8.525 -20.036  -1.884
      ATOM     28  HA  LEU     2      10.867 -22.070  -2.576
      ATOM     29 1HB  LEU     2       8.746 -21.553  -4.685
      ATOM     30 2HB  LEU     2      10.152 -22.623  -4.903
      ATOM     31  HG  LEU     2       7.969 -23.019  -2.854
      ATOM     32 1HD1 LEU     2       7.705 -23.310  -5.553
      ATOM     33 2HD1 LEU     2       8.376 -24.899  -5.114
      ATOM     34 3HD1 LEU     2       6.870 -24.328  -4.356
      ATOM     35 1HG2 LEU     2       9.162 -24.699  -2.016
      ATOM     36 2HG2 LEU     2       9.673 -25.263  -3.625
      ATOM     37 3HG2 LEU     2      10.558 -23.944  -2.822
 
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