

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     1 CONFIDENCE .4
HETATM    1  O1  ARA   705      70.426  18.914  23.232                
HETATM    2  O2  ARA   705      68.187  20.169  20.961                
HETATM    3  O3  ARA   705      67.952  22.486  23.146                
HETATM    4  O4  ARA   705      68.294  19.072  24.130                
HETATM    5  O5  ARA   705      65.793  20.291  25.041                
HETATM    6  C1  ARA   705      69.054  19.055  22.942                
HETATM    7  C2  ARA   705      68.754  20.382  22.264                
HETATM    8  C3  ARA   705      67.780  21.087  23.194                
HETATM    9  C4  ARA   705      68.134  20.493  24.522                
HETATM   10  C5  ARA   705      67.056  20.736  25.565                
HETATM   11  C6  ARA   705      71.016  17.734  22.651                
ENDMDL
