Explanation of the Ocker docking results:

Each file is named based on the protein system it is derived from i.e 1M48, 1PY2 etc.

I have constructed the loop receptor using 1M48 and spliced in the NMR loops from residues 

Residues 75-80 are taken from the NMR structure 1irl.

the first 3 residues are also taken from the NMR structure.

All ligands are then docked to this structure using several methods. 

1. straight docking with spheres [structurename]
2. Straight docking with spheres + the query (interacting sidechains from the receptor) added to supplement the spheres [structurename_withQuery]
3. Flexible overlay using the query only.  [structurename_flexibleOverlay]



Contents of the dirs:

Ocker.out	: scores of each poise from docking (top 25) with pre and post optimisation
OckerConsensus.out	: Scores of the best poise chosen with consensus
OckerConsensusMMFF.out	: Scores of the best poise chosen with consensus and MMFF, on MMFF poises
OckerConsensusMMFFDocked.oeb	: Orientation of the best consensus with MMFF 
OckerMMFF.out	: Scores of the best poise chosen with MMFF alone
OckerOptDockedPoise.mol2		: Debug poise from optimisation
ScoreData.log	: Debug file with scores of all poises generated during docking
checkpoint	: Checkpoint file
debug_0_preoptLigand.mol2	: Debug geometry file 
dockedLigand.mol2	: Orientations of the top 25 poises before MMFF optimisation
dockedLigand_opt.mol2	:  Orientations of the top 25 poises optimised with MMFF
flexible.param	: Parameter file for the docking run
flexible.param~
internalPoises.mol2	: All geometry generated during the run.
ocker.log	: Results of the docking run, the log file
proteinExtentsMol.pdb	: PDB representation of the sphere extents for multiple starts
proteinShapeMol.pdb	: PDB representation of the spheres