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1 <tool id="ctb_spectrophore_search" name="Spectrophores(TM) search:" version="1.0">
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2 <description>similarity search based on 1D chemical features</description>
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3 <requirements>
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4 <requirement type="package" version="2.3.2">openbabel</requirement>
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5 <requirement type="package" version="1.7.1">numpy</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8 <![CDATA[
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9 ob_spectrophore_search.py
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10 --target $target
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11 --library $library
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12 --output $outfile
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13 --column $column
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param name="target" type="data" format="sdf" label="Target molecule in SDF format (it must contain its Spectrophores(TM) stored as meta-data)"/>
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18 <param name="library" type="data" format="tabular" label="Tabular file with pre-computed Spectrophores(TM) in one column"/>
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19 <param name="column" label="Specify the column number containing the Spectrophores(TM) descriptors" type="data_column" data_ref="library" accept_default="true" />
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20 </inputs>
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21 <outputs>
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22 <data format="tabular" name="outfile"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="target" ftype="sdf" value="CID2244_with_spectrophore.sdf"/>
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27 <param name="library" value="lib.tabular" />
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28 <param name="column" value="8" />
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29 <output name="outfile" ftype="tabular" file="ob_spectrophore_search.tabular" />
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30 </test>
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31 </tests>
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32 <help>
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33 <![CDATA[
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34
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35 .. class:: infomark
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36
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37 **What does this tool do?**
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38
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39 This tool computes the Euclidean distance between the Spectrophores(TM) descriptors of the target to each molecule stored in the library.
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40
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41 |Spectrophores (TM)| search
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42 |Spectrophores (TM)| is a screening technology by Silicos_ which converts three-dimensional molecular property data into one-dimensional spectra. Typical characteristics that can be converted include electrostatic potentials, molecular shape, lipophilicity, hardness and softness potentials. The computation is independent of the position and orientation of a molecule and allows an easy comparison of |Spectrophores (TM)| of different molecules.
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43
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44 Molecules with similar three-dimensional properties and shape, and therefore also similar biological activities, always have similar |Spectrophores (TM)|. As a result this technique is a very powerful tool to investigate the similarity of molecules and can be applied as a screening tool for molecular databases, virtual screening, and database characterisations.
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45
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46 *Advantages:*
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47
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48 - |Spectrophores (TM)| can realistically compute ligand-protein interactions based on aforementioned molecular descriptors
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49 - |Spectrophores (TM)| can be applied in both a ligand- or target-based setting
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50 - |Spectrophores (TM)| can distinguish, if needed, between the different enantiomers of stereo-selective compounds
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51 - |Spectrophores (TM)| can be computed fast
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52
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53 .. |Spectrophores (TM)| unicode:: Spectrophores U+2122
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54
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55 -----
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56
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57 .. class:: warningmark
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58
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59 **Hint** this tool is useful to select compounds with similar chemical features to a target, but accounting for the discovery of diverse scaffolds. This is in contrast to the results expected in a similarity search based on atom connectivity.
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60
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61 -----
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62
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63 .. class:: infomark
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64
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65 **Input**
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66
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67 The target molecule must be a SD formatted file with the |Spectrophores (TM)| descriptors stored as metadata. Such files can be generated using the *Compute physico-chemical properties* tool.
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68
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69 -----
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70
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71 .. class:: infomark
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72
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73 **Output**
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74
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75 The library of compounds is a tabular file with one line per compound. One column contains the |Spectrophores (TM)| descriptors.
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76
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77 -----
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78
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79 .. class:: infomark
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80
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81 **Cite**
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82
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83 N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_
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84
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85 Silicos_ - |Spectrophores (TM)| is a registered tool implemented in the open-source OpenBabel.
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86
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87 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
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88 .. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html
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89
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90 ]]>
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91 </help>
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92 </tool>
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