

PFRMAT DKF1
TARGET T0013
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 .3
HETATM    1  O1  ARA   705      71.129  18.903  22.783                
HETATM    2  O2  ARA   705      68.633  20.037  20.726                
HETATM    3  O3  ARA   705      68.308  22.198  23.055                
HETATM    4  O4  ARA   705      69.054  18.790  23.812                
HETATM    5  O5  ARA   705      66.442  20.385  24.833                
HETATM    6  C1  ARA   705      69.733  18.915  22.583                
HETATM    7  C2  ARA   705      69.259  20.238  22.004                
HETATM    8  C3  ARA   705      68.281  20.788  23.030                
HETATM    9  C4  ARA   705      68.777  20.164  24.296                
HETATM   10  C5  ARA   705      67.749  20.238  25.413                
HETATM   11  C6  ARA   705      71.703  17.582  22.734                
ENDMDL
