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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML EXPERIMENTAL 970324//EN"><HTML><HEAD><META NAME="GENERATOR" CONTENT="Adobe FrameMaker 5.5/HTML Export Filter"><LINK REL="STYLESHEET" HREF="Manual.css"><TITLE> Orientation Search</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H2 CLASS="Heading-3"><A NAME="pgfId=6631"> </A><A NAME="30227"> </A><A NAME="marker=59138"> </A>Orientation Search</H2><P CLASS="Body"><A NAME="pgfId=6654"> </A>dock version 4.0 has a new orientation search algorithm, or matching algorithm, which is more robust than before (see Ewing and Kuntz [<A HREF="Manual.14.html#13035" CLASS="XRef">6</A>]). An orientation search is requested with the <A HREF="Manual.19.html#34562" CLASS="XRef">orient_ligand</A> parameter. The published search technique has been further extended so that the amount of orientation sampling can be controlled in two ways:</P><UL><LI CLASS="Body-Bullet"><A NAME="pgfId=6668"> </A><A HREF="Manual.e.html#35765" CLASS="XRef">Automated Matching</A> --Specify the number of orientations, and dock will generate matches until enough orientations passing the bump filter have been formed. Matches are formed best first, with respect to the difference in the ligand and site point internal distances.</LI><LI CLASS="Body-Bullet"><A NAME="pgfId=11309"> </A><A HREF="Manual.e.html#26030" CLASS="XRef">Manual Matching</A> --Specify the distance and node parameters, and dock will generate all the matches which satisfy them. The number of orientations scored is equal to the total matches minus the orientations discarded by the bump filter.</LI></UL><P CLASS="Body"><A NAME="pgfId=6669"> </A>There are a number of sophisticated options available to tailor the orientation search. These options include:</P><UL><LI CLASS="Body-Bullet"><A NAME="pgfId=10629"> </A><A HREF="Manual.e.html#36138" CLASS="XRef">Random Search</A></LI><LI CLASS="Body-Bullet"><A NAME="pgfId=10637"> </A><A HREF="Manual.e.html#36641" CLASS="XRef">Degeneracy Checking</A></LI><LI CLASS="Body-Bullet"><A NAME="pgfId=10641"> </A><A HREF="Manual.e.html#38872" CLASS="XRef">Ligand Mirroring</A></LI><LI CLASS="Body-Bullet"><A NAME="pgfId=10656"> </A><A HREF="Manual.e.html#85567" CLASS="XRef">Chemical Matching</A></LI><LI CLASS="Body-Bullet"><A NAME="pgfId=10646"> </A><A HREF="Manual.e.html#75586" CLASS="XRef">Critical Points</A></LI></UL><P CLASS="Body"><A NAME="pgfId=11046"> </A>Multiple orientations may be written out for each molecule using the <A HREF="Manual.19.html#20966" CLASS="XRef">write_orientations</A> parameter, otherwise only the best orientation is recorded. A ranked list of the orientations may be written using the <A HREF="Manual.19.html#23984" CLASS="XRef">rank_orientations</A> parameter. Otherwise, all orientations passing a score cutoff are written out. The score cutoff is specified with the <A HREF="Manual.19.html#27692" CLASS="XRef">contact_maximum</A> parameter and so on for each type of scoring. If <A HREF="Manual.19.html#20966" CLASS="XRef">write_orientations</A> is requested without scoring, then all orientations are written.</P><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=11295"> </A><A NAME="35765"> </A><A NAME="marker=11633"> </A>Automated Matching</H3><P CLASS="Body"><A NAME="pgfId=11299"> </A>With <A HREF="Manual.19.html#37805" CLASS="XRef">automated_matching</A>, dock performs the same amount of orientation searching on each molecule. If the <A HREF="Manual.19.html#40677" CLASS="XRef">match_receptor_sites</A> parameter is set, then <A HREF="Manual.e.html#33347" CLASS="XRef">Manual Matching</A> is used as a black box engine for the orientation search (otherwise a <A HREF="Manual.e.html#36138" CLASS="XRef">Random Search</A> is performed). The only sampling parameter needed is the <A HREF="Manual.19.html#32044" CLASS="XRef">maximum_orientations</A> parameter, which is the number of desired orientations which survive the bump filter. Matches are formed in order of the smallest distance error first, so that the highest quality orientations are guaranteed to come sooner rather than later. This method of control is incredibly easy. It is most appropriate when docking a single molecule. It should not be used for database docking, since manual matching performs better because it biases the amount of sampling depending on the size and shape of the ligand. In addition, if the user wishes to use advanced matching features, like <A HREF="Manual.e.html#85567" CLASS="XRef">Chemical Matching</A> and <A HREF="Manual.e.html#75586" CLASS="XRef">Critical Points</A>, then manual matching must be used.</P></DIV><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=6676"> </A><A NAME="33347"> </A><A NAME="26030"> </A><A NAME="marker=11634"> </A>Manual Matching</H3><P CLASS="Body"><A NAME="pgfId=6677"> </A>If the <A HREF="Manual.19.html#40677" CLASS="XRef">match_receptor_sites</A> parameter is set but not the <A HREF="Manual.19.html#37805" CLASS="XRef">automated_matching</A> parameter, then manual matching is performed. It is controlled by the match parameters listed in <A HREF="Manual.e.html#30532" CLASS="XRef">Table 4.</A> The matching parameters provide an intuitive way to control sampling. When multiple molecules are docked, matching will bias sampling towards molecules with more internal distance similarity with the receptor site points. The additional chemical and critical matching constraints provide a way to prune matching and further bias sampling towards more interesting molecules.</P><H3 CLASS="Table"><A NAME="pgfId=11359"> </A>Table 4. <A NAME="30532"> </A>Description of Matching Parameters</H3><TABLE><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=6772"> </A><A HREF="Manual.19.html#31851" CLASS="XRef"></A>distance_tolerance</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=6774"> </A>The distance tolerance can be viewed as the uncertainty in the distance comparisons or site point positions. The more generous the uncertainty in the distance comparisons, the more sampling will be performed. This parameter should be the first parameter to adjust if you need to change the amount of sampling.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=6776"> </A><A HREF="Manual.19.html#36956" CLASS="XRef"></A>distance_minimum</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=6778"> </A>The distance minimum allows matching to focus on the longer distances which convey more information about molecule or site shape. This value can be conveniently set large enough to discard atoms directly bonded to each other. When docking large molecules, this value can be set higher.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=6780"> </A><A HREF="Manual.19.html#24742" CLASS="XRef"></A>nodes_minimum</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=6782"> </A>The minimum number of nodes must be at least three to specify a unique rigid transformation. A value of four or more will allow every match to include information about chirality. Match chirality can be used to explore the mirror image of a molecule for docking. The higher this parameter, the better the ligand atoms in the match represent the entire molecule.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=6784"> </A><A HREF="Manual.19.html#16594" CLASS="XRef"></A>nodes_maximum</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=6786"> </A>This value may be set arbitrarily high to prevent it from influencing matching. It may be set equal to the nodes minimum when performing pharmacophore-style matching if only a few specific site interactions are of interest.</P></TD></TR></TABLE></DIV><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=6634"> </A><A NAME="36138"> </A><A NAME="marker=11635"> </A>Random Search</H3><P CLASS="Body"><A NAME="pgfId=8376"> </A>The <A HREF="Manual.19.html#27719" CLASS="XRef">random_search</A> option is intended for advanced users. If <A HREF="Manual.19.html#40677" CLASS="XRef">match_receptor_sites</A> is also set then random matching is performed, in which ligand centers and receptor sites are randomly matched regardless of internal distances. Otherwise, a random transformation search is performed, in which ligands are randomly rotated and translated within the rectangular box enclosing all the site points. Both methods could be employed when the user is concerned about the quality of the site point positions, or would simply like to try a richer set of generated orientations.</P><DIV><H6 CLASS="Heading-5"><A NAME="pgfId=8792"> </A><A NAME="marker=11636"> </A>Site Point Construction</H6>?? 快捷鍵說明
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