help/html/webServices/proteinDisorder.html

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  20 <head>
  21 <title>JABAWS Protein Disorder Prediction Services</title>
  22 </head>
  23 <body>
  24         <p>
  25                 <strong>JABAWS Protein Disorder Prediction Services</strong> <br />
  26                 The <strong>Web Services&rarr;Disorder</strong> menu in the alignment
  27                 window allows access to protein disorder prediction services provided
  28                 by the configured <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS
  29                         servers</a>. Each service operates on sequences in the alignment to
  30                 identify regions likely to be unstructured or flexible, or
  31                 alternately, fold to form globular domains.
  32         </p>
  33         <p>
  34                 Predictor results include both <a href="../features/seqfeatures.html">sequence
  35                         features</a> and sequence associated <a
  36                         href="../features/annotation.html">alignment annotation</a> rows.
  37                 Features display is controlled from the <a
  38                         href="../features/featureSettings.html">Feature Settings</a> dialog
  39                 box. Clicking on the ID for a disorder prediction annotation row will
  40                 highlight or select (if double clicked) the associated sequence for
  41                 that row. You can also use the <em>Sequence Associated</em> option in
  42                 the <a href="../colourSchemes/annotationColouring.html">Colour By
  43                         Annotation</a> dialog box to colour sequences according to the results of
  44                 predictors shown as annotation rows.
  45         </p>
  46         <p>JABAWS 2.0 provides four disorder predictors which are described
  47                 below:</p>
  48         <ul>
  49                 <li><a href="#disembl">DisEMBL</a></li>
  50                 <li><a href="#iupred">IUPred</a></li>
  51                 <li><a href="#ronn">RONN</a></li>
  52                 <li><a href="#globplot">GlobPlot</a></li>
  53         </ul>
  54         <p>
  55                 <strong><a name="disembl"></a><a href="http://dis.embl.de/">DisEMBL
  56                                 (Linding et al., 2003)</a> </strong> <br /> DisEMBL is a set of machine-learning
  57                 based predictors trained to recognise disorder-related annotation
  58                 found on PDB structures.
  59         </p>
  60         <table border="1">
  61                 <tr>
  62                         <td><strong>Name</strong></td>
  63                         <td><strong>Annotation type</strong></td>
  64                         <td><strong>Description</strong></td>
  65                 </tr>
  66                 <tr>
  67                         <td><strong>COILS</strong></td>
  68                         <td>Sequence Feature &amp;<br />Annotation Row
  69                         </td>
  70                         <td>Predicts loops/coils according to DSSP definition<a
  71                                 href="#dsspstates">[1]</a>.<br />Features mark range(s) of residues
  72                                 predicted as loops/coils, and annotation row gives raw value for
  73                                 each residue. Value over 0.516 indicates loop/coil.
  74                         </td>
  75                 </tr>
  76                 <tr>
  77                         <td><strong>HOTLOOPS</strong></td>
  78                         <td>Sequence Feature &amp;<br />Annotation Row
  79                         </td>
  80                         <td>&quot;Hot loops constitute a refined subset of <strong>COILS</strong>,
  81                                 namely those loops with a high degree of mobility as determined from
  82                                 C&alpha; temperature factors (B factors). It follows that highly
  83                                 dynamic loops should be considered protein disorder.&quot;<br />
  84                                 Features mark range(s) of residues predicted to be hot loops and
  85                                 annotation row gives raw value for each residue. Values over 0.6
  86                                 indicates hot loop.
  87                         </td>
  88                 </tr>
  89                 <tr>
  90                         <td><strong>REMARK465</strong></td>
  91                         <td>Sequence Feature &amp;<br />Annotation Row
  92                         </td>
  93                         <td>&quot;Missing coordinates in X-ray structure as defined by
  94                                 remark465 entries in PDB. Nonassigned electron densities most often
  95                                 reflect intrinsic disorder, and have been used early on in disorder
  96                                 prediction.&quot;<br /> Features gives range(s) of residues
  97                                 predicted as disordered, and annotation row gives raw value for each
  98                                 residue. Value over 0.1204 indicates disorder.
  99                         </td>
 100                 </tr>
 101         </table>
 102
 103         <p>
 104                 <a name="dsspstates"></a>[1]. DSSP Classification: &alpha;-helix (H),
 105                 310-helix (G), &beta;-strand (E) are ordered, and all other states
 106                 (&beta;-bridge (B), &beta;-turn (T), bend (S), &pi;-helix (I), and
 107                 coil (C)) considered loops or coils.
 108         </p>
 109
 110
 111         <p>
 112                 <strong><a name="ronn"></a><a
 113                         href="http://www.strubi.ox.ac.uk/RONN">RONN</a></strong> <em>a.k.a.</em>
 114                 Regional Order Neural Network<br />This predictor employs an approach
 115                 known as the 'bio-basis' method to predict regions of disorder in
 116                 sequences based on their local similarity with a gold-standard set of
 117                 disordered protein sequences. It yields a set of disorder prediction
 118                 scores, which are shown as sequence annotation below the alignment.
 119         </p>
 120         <table border="1">
 121                 <tr>
 122                         <td><strong>Name</strong></td>
 123                         <td><strong>Annotation type</strong></td>
 124                         <td><strong>Description</strong></td>
 125                 </tr>
 126                 <tr>
 127                         <td><strong>JRonn</strong>[2]</td>
 128                         <td>Annotation Row</td>
 129                         <td>RONN score for each residue in the sequence. Scores above
 130                                 0.5 identify regions of the protein likely to be disordered.</td>
 131                 </tr>
 132         </table>
 133         <p>
 134                 <em>[2]. JRonn denotes the score for this server because JABAWS
 135                         runs a Java port of RONN developed by Peter Troshin and distributed
 136                         as part of <a href="http://www.biojava.org/">Biojava 3</a>
 137                 </em>
 138         </p>
 139         <p>
 140                 <strong><a name="iupred"></a><a
 141                         href="http://iupred.enzim.hu/Help.php">IUPred</a></strong><br /> IUPred
 142                 employs an empirical model to estimate likely regions of disorder.
 143                 There are three different prediction types offered, each using
 144                 different parameters optimized for slightly different applications. It
 145                 provides raw scores based on two models for predicting regions of
 146                 'long disorder' and 'short disorder'. A third predictor identifies
 147                 regions likely to form structured domains.
 148         </p>
 149         <table border="1">
 150                 <tr>
 151                         <td><strong>Name</strong></td>
 152                         <td><strong>Annotation type</strong></td>
 153                         <td><strong>Description</strong></td>
 154                 </tr>
 155                 <tr>
 156                         <td><strong>Long disorder</strong></td>
 157                         <td>Annotation Row</td>
 158                         <td>Prediction of context-independent global disorder that
 159                                 encompasses at least 30 consecutive residues of predicted disorder.
 160                                 Employs a 100 residue window for calculation.<br />Values above 0.5
 161                                 indicates the residue is intrinsically disordered.
 162                         </td>
 163                 </tr>
 164                 <tr>
 165                         <td><strong>Short disorder</strong></td>
 166                         <td>Annotation Row</td>
 167                         <td>Predictor for short, (and probably) context-dependent,
 168                                 disordered regions, such as missing residues in the X-ray structure
 169                                 of an otherwise globular protein. Employs a 25 residue window for
 170                                 calculation, and includes adjustment parameter for chain termini
 171                                 which favors disorder prediction at the ends.<br />Values above 0.5
 172                                 indicate short-range disorder.
 173                         </td>
 174                 </tr>
 175                 <tr>
 176                         <td><strong>Structured domains</strong></td>
 177                         <td>Sequence Feature</td>
 178                         <td>Features highlighting likely globular domains useful for
 179                                 structure genomics investigation. <br />Post-analysis of disordered
 180                                 region profile to find continuous regions confidently predicted to
 181                                 be ordered. Neighbouring regions close to each other are merged,
 182                                 while regions shorter than the minimal domain size of at least 30
 183                                 residues are ignored.
 184                         </td>
 185                 </tr>
 186         </table>
 187         <p>
 188                 <strong><a name="globplot"></a><a
 189                         href="http://globplot.embl.de/">GLOBPLOT</a></strong><br /> Defines regions
 190                 of globularity or natively unstructured regions based on a running sum
 191                 of the propensity of residues to be structured or unstructured. The
 192                 propensity is calculated based on the probability of each amino acid
 193                 being observed within well defined regions of secondary structure or
 194                 within regions of random coil. The initial signal is smoothed with a
 195                 Savitzky-Golay filter, and its first order derivative computed.
 196                 Residues for which the first order derivative is positive are
 197                 designated as natively unstructured, whereas those with negative
 198                 values are structured.<br />
 199         <table border="1">
 200                 <tr>
 201                         <td><strong>Name</strong></td>
 202                         <td><strong>Annotation type</strong></td>
 203                         <td><strong>Description</strong></td>
 204                 </tr>
 205                 <tr>
 206                         <td><strong>Disordered Region</strong></td>
 207                         <td>Sequence Feature</td>
 208                         <td><br />Sequence features marking range(s) of residues with
 209                                 positive dydx values (correspond to the #Disorder column from JABAWS
 210                                 results)</td>
 211                 </tr>
 212                 <tr>
 213                         <td><strong>Globular Domain</strong>
 214                         <td>Sequence Feature</td>
 215                         <td>Putative globular domains</td>
 216                 </tr>
 217                 <tr>
 218                         <td><strong>Dydx</strong></td>
 219                         <td>Annotation row</td>
 220                         <td>First order derivative of smoothed score. Values above 0
 221                                 indicates residue is disordered.</td>
 222                 </tr>
 223                 <tr>
 224                         <td><strong>Smoothed Score<br />Raw Score
 225                         </strong></td>
 226                         <td>Annotation Row</td>
 227                         <td>The smoothed and raw scores used to create the differential
 228                                 signal that indicates the presence of unstructured regions.<br /> <em>These
 229                                         are hidden by default, but can be shown by right-clicking on the
 230                                         alignment annotation panel and selecting <strong>Show
 231                                                 hidden annotation</strong>
 232                         </em>
 233                         </td>
 234                 </tr>
 235         </table>
 236         <p>
 237                 <em>Documentation and thresholds for the JABAWS Disorder
 238                         predictors adapted from a personal communication by Nancy Giang,
 239                         2012.</em>
 240         </p>
 241 </body>
 242 </html>