

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     1 CONFIDENCE 0.4
ATOM      1 C1   AIC   336      12.986   3.387  91.033                
ATOM      2 N1   AIC   336      13.310   2.227  91.580                
ATOM      3 C2   AIC   336      12.739   2.152  92.744                
ATOM      4 N2   AIC   336      12.218   3.246  93.053                
ATOM      5 C3   AIC   336      12.301   4.132  91.930                
ATOM      6 C4   AIC   336      15.520  -0.608  92.007                
ATOM      7 C5   AIC   336      15.323   0.930  92.013                
ATOM      8 C6   AIC   336      14.131   1.142  91.058                
ATOM      9 O2   AIC   336      13.440  -0.143  91.061                
ATOM     10 C7   AIC   336      14.068  -1.106  91.942                
ATOM     11 C8   AIC   336      13.416  -1.242  93.356                
ATOM     12 O3   AIC   336      16.310  -1.018  90.856                
ATOM     13 O4   AIC   336      16.504   1.600  91.569                
ATOM     14 N3   AIC   336      13.233   3.793  89.807                
ATOM     15 C9   AIC   336      11.756   5.503  91.754                
ATOM     16 N4   AIC   336      11.252   6.164  92.756                
ATOM     17 O5   AIC   336      11.778   6.022  90.645                
ATOM     18 O1   AIC   336      13.999  -0.341  94.297                
ATOM     19 P1   AIC   336      13.671  -0.112  95.847                
ATOM     20 O6   AIC   336      12.090   0.112  96.008                
ATOM     21 O7   AIC   336      13.906  -1.458  96.657                
ATOM     22 O8   AIC   336      14.553   1.043  96.509                
TER      23      AIC   336 
ENDMDL
