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:
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
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