Dock Ligand Clustering

DOCK 3.6 Ligand Clustering

• branch of DOCK_3.6
• Contributed by Niu Huang's lab
• Currently in the niu-nibs-clustering branch, ready for use
• Replacement for single mode
• Example INDOCK file parameters, add to your current INDOCK file

#
################################################################################
#                         POSE_CLUSTERING
#
pose_clustering                     yes
# "yes/no" General switch of pose clustering (default: no)
pose_clustering_detail              no
# "yes/no" Switch of print out detail infomation (default: no)
pose_clustering_method              0
# 0---------Write all the poses
# 1---------Clustering method based on KGS penalty function
# 2---------Clustering method based on ratio of RANK and RMSD
pose_clustering_cutoff              1.1
# pre-determined variable for clustering cutoff
# In method 0, the cutoff is unused.
# In method 1, the cutoff is unused.
# In method 2, the cutoff is Nc.
################################################################################
# cutoff in pose_clustering for saving resource
#pose_clustering_RMSD_cutoff
#pose_clustering_energy_cutoff       no
pose_clus_inputno_cutoff      0
# number: input number cutoff; 0: no; -1: rotatable bond based (NA)
# number of poses to be clustered according to energy rank
# for method 0, it is also used.
pose_clus_outputno_cutoff     0
# number: output number cutoff; 0: no
# number of clustered poses being written out according to energy rank
# for method 0, it is also used.
################################################################################

Currently installed in

~xyz/dockenv/bin/Linux/ligandclustering/

Bonus: A version compiled with nsize=193 for use with Qnifft [[1]] is in

~xyz/dockenv/bin/Linux/ligandclustering-qnifft/

Or where ~xyz/dockenv is your $DOCK_BASE