[Dock-fans] Failed Docking even after relaxing params

Sudipto Mukherjee sudmukh at yahoo.com
Mon Nov 3 07:20:08 PST 2014

Hi Amr,
Try redocking those four complexes without the bump filter. From the verbose dock output, it looks like a lot of your partially grown conformers were pruned by the bump filter. 
We typically use < 100 spheres in the binding site. Is there a reason why you are using so many spheres? Despite starting with so many spheres and consequently a very large number of cliques during anchor orienting, the flexible docking calculation stage starts with only 23,10 and 9 anchor orients for each anchor after clustering.  Regards
Sudipto Mukherjee, PhDDept. of Chemistry, Temple University1901 N 13th St, Philadelphia, PA 19122 

     On Monday, November 3, 2014 5:26 AM, #AMR ALI MOKHTAR ALHOSSARY# <AMRA0001 at e.ntu.edu.sg> wrote:

  <!--#yiv3627701926 _filtered #yiv3627701926 {font-family:"Cambria Math";panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv3627701926 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;} _filtered #yiv3627701926 {font-family:"Baskerville Old Face";panose-1:2 2 6 2 8 5 5 2 3 3;}#yiv3627701926 #yiv3627701926 p.yiv3627701926MsoNormal, #yiv3627701926 li.yiv3627701926MsoNormal, #yiv3627701926 div.yiv3627701926MsoNormal {margin:0cm;margin-bottom:.0001pt;font-size:11.0pt;font-family:"Calibri", sans-serif;}#yiv3627701926 a:link, #yiv3627701926 span.yiv3627701926MsoHyperlink {color:#0563C1;text-decoration:underline;}#yiv3627701926 a:visited, #yiv3627701926 span.yiv3627701926MsoHyperlinkFollowed {color:#954F72;text-decoration:underline;}#yiv3627701926 span.yiv3627701926EmailStyle17 {font-family:"Calibri", sans-serif;color:windowtext;}#yiv3627701926 .yiv3627701926MsoChpDefault {font-family:"Calibri", sans-serif;} _filtered #yiv3627701926 {margin:72.0pt 90.0pt 72.0pt 90.0pt;}#yiv3627701926 div.yiv3627701926WordSection1 {}-->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 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|  Mobile: +65-94572816     |

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