[Dock-fans] Failed Docking even after relaxing params

#AMR ALI MOKHTAR ALHOSSARY# AMRA0001 at e.ntu.edu.sg
Mon Nov 3 02:25:53 PST 2014


Hi
While docking PDBbind 2014 core collection, four of the receptor-ligand complexes failed to find a suitable conformation, using the same parameter value of the application tutorial.

Even after relaxing the parameters: min_anchor_size to 6, max_orientations to 50000, pruning_max_orients to 1000, pruning_clustering_cutoff to 25; four complexes fail to find any suitable conformations. They are namely 3PWW, 1NVQ, 2PQ9, 2YGE.

May I have any recommendations?
I am attaching the output of one of them for your reference.

Amr


Best Regards,
Amr AL-HOSSARY

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Amr Ali AL-HOSSARY |   Ph.D. Student | International PhD program in Computational Biology and Bioinformatics | School of Computer Engineering |   Nanyang Technological University | Singapore (GMT+8) |  Email:  aalhossary at pmail.ntu.edu.sg<mailto:aalhossary at pmail.ntu.edu.sg> |  Mobile: +65-94572816




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