GETATOMS: Computing side chain conformations by simulated annealing
with frozen main chain atoms is release as one of new program in
protein structure prediction suit: sspal, nnssp, ssenvid
(3D-comp, FOLD and H-model will appear soon also):
Available at www.softberry.com
http://www.softberry.com/berry.phtml?topic=prot_new&prg=GETATOMS
GETATOMS is a program of modelling 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 estimate
quality of produced 3D structure using several scores:
Steric_Score a la JMB (1997), 267, 1268-1282
VDW_Score a la JMB(1981) v.153,p.1087-1109
and Bump Score is number of atomic pairs having sterically forbiden 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
query sequence and template protein sequence in several formats.
For example if we have 4hhb (A) sequence as query 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
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
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