

PFRMAT DKF1
TARGET T0039
AUTHOR 6682-2204-3506 Bernd Kramer, GMD-SCAI, Bernd.Kramer@gmd.de
AUTHOR 6682-2204-3506 Thomas Lengauer, GMD-SCAI, Lengauer@gmd.de
AUTHOR 6682-2204-3506 Matthias Rarey, GMD-SCAI, Rarey@gmd.de
REMARK ===================================================================
REMARK 1.Preparation of input data
REMARK   The ligand is generated and energy minimized to fall in an 
REMARK   arbitrary low-energy conformation. Favorable torsion angles at 
REMARK   rotatable bonds, interaction types, and interaction geometries 
REMARK   are automatically assigned.
REMARK   The active site of the protein is selected manually by comparing
REMARK   the protein structure to complexes where the same protein is
REMARK   involved (typically 8-10 A around the ligand). Hydrogens at
REMARK   hydrogen bond donors and acceptors are added in standard 
REMARK   geometries automatically. Interaction types and interaction 
REMARK   geometries are also assigned automatically.
REMARK 2.Docking
REMARK   Complexes are generated using our docking software FlexX (see
REMARK   Ref.). FlexX is a docking tool based on an incremental 
REMARK   construction algorithm producing results in approximately
REMARK   1-3 minutes for one pair of a receptor and a ligand molecule. 
REMARK   No refinement of the produced structures is performed.
REMARK 3.Selection of models
REMARK   The selection of a set of models and the assignment of 
REMARK   confidences is done manually again. Here we have considered
REMARK   phenomena like intramolecular hydrogen bonds which are not 
REMARK   modeled yet. FlexX' energy predictions for the different models
REMARK   are used as a guideline for the selection.
REMARK ===================================================================
REMARK References: 
REMARK   Matthias Rarey, Stephan Wefing and Thomas Lengauer:
REMARK   Placement of medium-sized molecular fragments into active sites
REMARK   of proteins, JCAMD (1996) 10, 41--54
REMARK
REMARK   Matthias Rarey, Bernd Kramer, Thomas Lengauer and Gerhard Klebe: 
REMARK   A Fast Flexible Docking Method using an Incremental Construction 
REMARK   Algorithm, JMB (1996) 261, 470--489
REMARK ===================================================================
MODEL     2 CONFIDENCE 0.4
ATOM      1 C1   AIC   336      14.189   3.031  87.873                
ATOM      2 N1   AIC   336      14.013   2.321  89.174                
ATOM      3 C2   AIC   336      13.744   3.329  90.151                
ATOM      4 N2   AIC   336      13.761   4.599  89.451                
ATOM      5 C3   AIC   336      14.040   4.351  88.051                
ATOM      6 C4   AIC   336      15.256  -0.211  91.259                
ATOM      7 C5   AIC   336      15.476   0.551  89.962                
ATOM      8 C6   AIC   336      14.064   0.926  89.566                
ATOM      9 O2   AIC   336      13.237   0.695  90.689                
ATOM     10 C7   AIC   336      13.764  -0.498  91.223                
ATOM     11 C8   AIC   336      13.174  -0.800  92.619                
ATOM     12 O3   AIC   336      16.007  -1.403  91.331                
ATOM     13 O4   AIC   336      16.124  -0.254  89.004                
ATOM     14 N3   AIC   336      14.477   2.276  86.669                
ATOM     15 C9   AIC   336      14.174   5.296  86.868                
ATOM     16 N4   AIC   336      13.120   5.600  86.162                
ATOM     17 O5   AIC   336      15.280   5.747  86.615                
ATOM     18 O1   AIC   336      13.992  -0.194  93.625                
ATOM     19 P1   AIC   336      13.658  -0.316  95.186                
ATOM     20 O6   AIC   336      13.657  -1.857  95.613                
ATOM     21 O7   AIC   336      14.764   0.472  96.033                
ATOM     22 O8   AIC   336      12.217   0.320  95.473                
TER      23      AIC   336 
ENDMDL
