GETATOMS: Computing side chain conformations by simulated annealing

webmaster at softberry.com webmaster at softberry.com
Fri Mar 29 14:35:50 EST 2002


  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
      

-------------------------------------------------
This mail sent through AceDSL WebMail (http://webmail.acedsl.com)

---




More information about the Molmodel mailing list