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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> Macromolecular Docking</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H2 CLASS="Heading-3"><A NAME="pgfId=8050"> </A><A NAME="13898"> </A>Macromolecular Docking</H2><P CLASS="Body"><A NAME="pgfId=11285"> </A>Though dock is typically used to process small molecules, it can be used to study the interactions of macromolecular ligands. The chief difference in protocol is that to use the <A HREF="Manual.19.html#40677" CLASS="XRef">match_receptor_sites</A> procedure for the <A HREF="Manual.e.html#30227" CLASS="XRef">Orientation Search</A>, then special ligand centers must be used to represent the ligand. This is signalled by setting the <A HREF="Manual.19.html#34261" CLASS="XRef">ligand_centers</A> parameter. The ligand centers must reside in a file identified with the <A HREF="Manual.19.html#36287" CLASS="XRef">ligand_center_file</A> parameter.</P><P CLASS="Body"><A NAME="pgfId=11393"> </A>The ligand centers may be constructed with <A HREF="Manual.20.html#17338" CLASS="XRef">sphgen</A>, using spheres to describe the positive image of the macromolecule. See Shoichet and Kuntz [<A HREF="Manual.14.html#22657" CLASS="XRef">26</A>], for examples and discussion of macromolecular docking.</P><P CLASS="Body"><A NAME="pgfId=11405"> </A>If multiple orientations are written to PDB formatted file, then the residue numbers are not disturbed. Normally, dock gives each orientation in the output PDB file a sequential residue number. However, if multiple substructures (residues) are present in the molecule input file, then this procedure is precluded.</P><DIV><H6 CLASS="New-Page"><A NAME="pgfId=4567"> </A> </H6></DIV><CENTER><P>⌨️ 快捷键说明
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