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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> What dock Can Do for You</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H3 CLASS="Heading-3"><A NAME="pgfId=127"> </A>What dock Can Do for You</H3><P CLASS="Body"><A NAME="pgfId=49271"> </A>The new version of dock can be used in many ways to aid in computational tasks. The following table, <A HREF="Manual.6.html#13615" CLASS="XRef">Table 1</A> lists how the new features can be combined together to accomplish different tasks. Only the basic tasks will be discussed in the <A HREF="Manual.7.html#32062" CLASS="XRef">Getting Started</A> section. Please refer to the <A HREF="Manual.d.html#27881" CLASS="XRef">Advanced Techniques</A> section (or follow the links contained with the table) for a discussion of each feature and refer to the <A HREF="Manual.html#16301" CLASS="XRef">Reference Manual</A> for a listing of all associated parameters.</P><P CLASS="Body"><A NAME="pgfId=50802"> </A> </P><TABLE><TR><TH ROWSPAN="1" COLSPAN="1"><H3 CLASS="Table"><A NAME="pgfId=50820"> </A>Table 1. Dock<A NAME="13615"> </A> Functionality</H3></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49308"> </A><A HREF="Manual.19.html#22201" CLASS="XRef">flexible_ligand</A></P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49313"> </A><A HREF="Manual.19.html#34562" CLASS="XRef">orient_ligand</A></P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49318"> </A><A HREF="Manual.19.html#35823" CLASS="XRef">score_ligand</A></P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49323"> </A><A HREF="Manual.19.html#37217" CLASS="XRef">multiple_ligands</A></P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49328"> </A><A HREF="Manual.19.html#35897" CLASS="XRef">chemical_screen</A></P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49333"> </A><A HREF="Manual.19.html#14818" CLASS="XRef">parallel_jobs</A></P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49338"> </A>Perform a <A HREF="Manual.f.html#31662" CLASS="XRef">Conformation Search</A> of a molecule.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49340"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49342"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49344"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49346"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49348"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49350"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49352"> </A>Generate configurations of a molecule in a site.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49354"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49356"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49358"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49360"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49362"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49364"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49369"> </A>Dock a flexible molecule (with <A HREF="Manual.f.html#37908" CLASS="XRef">Anchor-First Search</A> optional).</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49371"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49373"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49375"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49377"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49379"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49381"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49383"> </A>Dock a database of flexible molecules.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49385"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49387"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49389"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49391"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49393"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49395"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49397"> </A>Generate conformations and compute internal scores.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49399"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49401"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49403"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49405"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49407"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49409"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49411"> </A>Generate conformations for a database of molecules.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49413"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49415"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49417"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49419"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49421"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49423"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49428"> </A>Key a database for a <A HREF="Manual.12.html#40576" CLASS="XRef">Chemical Screen</A> (similarity or pharmacophore).</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49430"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49432"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49434"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49436"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49438"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49440"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49445"> </A>Parse a database, processing each conformer by <A HREF="Manual.11.html#22734" CLASS="XRef">Parallel Jobs</A>.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49447"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49449"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49451"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49453"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49455"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49457"> </A>X</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49462"> </A>Perform an <A HREF="Manual.e.html#30227" CLASS="XRef">Orientation Search</A> of a molecule in a site.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49464"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49466"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49468"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49470"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49472"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49474"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49476"> </A>Perform rigid docking of the input conformation of a molecule.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49478"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49480"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49482"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49484"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49486"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49488"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49490"> </A>Perform rigid docking of a database.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49492"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49494"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49496"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49498"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49500"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49502"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49510"> </A>Perform <A HREF="Manual.10.html#30177" CLASS="XRef">Scoring</A> or <A HREF="Manual.10.html#23381" CLASS="XRef">Score Optimization</A> of input position of a molecule.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49512"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49514"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49516"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49518"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49520"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49522"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49524"> </A>Score/minimize database of molecules or molecule configurations.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49526"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49528"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49530"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49532"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49534"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49536"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49538"> </A>Read/write a database of molecules (file format conversion).</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49540"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49542"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49544"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49546"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49548"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49550"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49555"> </A>Filter a database by <A HREF="Manual.12.html#40576" CLASS="XRef">Chemical Screen</A> (similarity or pharmacophore).</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49557"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49559"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49561"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49563"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49565"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49567"> </A> </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=49572"> </A>Parse a database, processing each molecule by <A HREF="Manual.11.html#22734" CLASS="XRef">Parallel Jobs</A>.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49574"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49576"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49578"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49580"> </A>X</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49582"> </A> </P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Table-Cell"><A NAME="pgfId=49584"> </A>X</P></TD></TR></TABLE><DIV><H6 CLASS="New-Page"><A NAME="pgfId=5247"> </A> </H6></DIV><CENTER><P>⌨️ 快捷键说明
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