<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:tahoma,new york,times,serif;font-size:10pt">Grzegorz,<br><br>Min Anchor size:<br>The default size of 40 atoms will cause Dock to select the largest anchor only for most molecules. Using a smaller anchor size rapidly increases the execution time though. min_anchor_size of 6 means the anchor can be as small as a single benzene ring. This parameter is somewhat analogous to the multiple_anchors parameter present in DOCK 4. Using multiple anchors can improve sampling in some cases, but mostly results in sampling similar conformers multiple times. Also, I would recommend using clustering when using a small min_anchor_size to prune the number of similar conformers sampled.<br><br>Clash_overlap:<br>DOCK computes clash overlap with the following formula:<br>if ( distance(atom_A, atom_B) < clash_overlap *( radius_atom_A + radius_atom_B ) ) assume
there is a clash<br><br>See the segment_clash_check() function in conf_gen.ccp for details.<br><div> </div><font size="2"><span style="font-family: tahoma,new york,times,serif;">Regards<br>Sudipto Mukherjee<br></span></font><font size="2"><span style="font-family: tahoma,new york,times,serif;"><span style="font-style: italic; color: rgb(82, 83, 48);">Graduate Student, Robert C. Rizzo Lab</span><br style="font-style: italic; color: rgb(82, 83, 48);"><span style="font-style: italic; color: rgb(82, 83, 48);">Dept. of Applied Math & Statistics, Stony Brook University</span><br style="font-style: italic; color: rgb(82, 83, 48);"><span style="font-style: italic; color: rgb(82, 83, 48);"></span></span></font><br><div style="font-family: tahoma,new york,times,serif; font-size: 10pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original Message ----<br>From: Grzegorz Popowicz
<popowicz@biochem.mpg.de><br>To: dock-fans@docking.org<br>Sent: Monday, August 6, 2007 5:39:21 AM<br>Subject: [Dock-fans] Anchor size and clashes elimination<br><br><div>Hi all!<br>1. The default size of an anchor in DOCK is 40 atoms this generates quite big <br>fragments as for beginning of docking (at least 480Da). I have tried smaller <br>anchors (8 atoms) with good results. Are there any rules governing selection <br>of anchor size?<br>2. Dock run with use_clash_overlap=no generates solutions with terrible <br>clashes (of course), however the predictions of known ligands binding are <br>very good in my case. With use_clash_overlap=yes and clash_overlap=0.5 (BTW. <br>What does percent of overlap mean?) there are no clushes but known ligands <br>are badly docked and scored much much worse than without clashes filter. Is <br>there any resonable explanation to this
fact?<br><br>Gregor<br>_______________________________________________<br>Dock-fans mailing list<br>Dock-fans@docking.org<br><a target="_blank" href="http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans">http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans</a><br></div></div><br></div></div><br>
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