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 or
  30                 currently selected region (<em>since Jalview 2.8.0b1</em>) to identify
  31                 regions likely to be unstructured or flexible, or alternately, fold to
  32                 form globular domains.
  33         </p>
  34         <p>
  35                 Predictor results include both <a href="../features/seqfeatures.html">sequence
  36                         features</a> and sequence associated <a
  37                         href="../features/annotation.html">alignment annotation</a> rows.
  38                 Features display is controlled from the <a
  39                         href="../features/featureSettings.html">Feature Settings</a> dialog
  40                 box. Clicking on the ID for a disorder prediction annotation row will
  41                 highlight or select (if double clicked) the associated sequence for
  42                 that row. You can also use the <em>Sequence Associated</em> option in
  43                 the <a href="../colourSchemes/annotationColouring.html">Colour By
  44                         Annotation</a> dialog box to colour sequences according to the results of
  45                 predictors shown as annotation rows.
  46         </p>
  47         <p>JABAWS 2.0 provides four disorder predictors which are described
  48                 below:</p>
  49         <ul>
  50                 <li><a href="#disembl">DisEMBL</a></li>
  51                 <li><a href="#iupred">IUPred</a></li>
  52                 <li><a href="#ronn">RONN</a></li>
  53                 <li><a href="#globplot">GlobPlot</a></li>
  54         </ul>
  55         <p>
  56                 <strong><a name="disembl"></a><a href="http://dis.embl.de/">DisEMBL
  57                                 (Linding et al., 2003)</a> </strong> <br /> DisEMBL is a set of machine-learning
  58                 based predictors trained to recognise disorder-related annotation
  59                 found on PDB structures.
  60         </p>
  61         <table border="1">
  62                 <tr>
  63                         <td><strong>Name</strong></td>
  64                         <td><strong>Annotation type</strong></td>
  65                         <td><strong>Description</strong></td>
  66                 </tr>
  67                 <tr>
  68                         <td><strong>COILS</strong></td>
  69                         <td>Sequence Feature &amp;<br />Annotation Row
  70                         </td>
  71                         <td>Predicts loops/coils according to DSSP definition<a
  72                                 href="#dsspstates">[1]</a>.<br />Features mark range(s) of residues
  73                                 predicted as loops/coils, and annotation row gives raw value for
  74                                 each residue. Value over 0.516 indicates loop/coil.
  75                         </td>
  76                 </tr>
  77                 <tr>
  78                         <td><strong>HOTLOOPS</strong></td>
  79                         <td>Sequence Feature &amp;<br />Annotation Row
  80                         </td>
  81                         <td>&quot;Hot loops constitute a refined subset of <strong>COILS</strong>,
  82                                 namely those loops with a high degree of mobility as determined from
  83                                 C&alpha; temperature factors (B factors). It follows that highly
  84                                 dynamic loops should be considered protein disorder.&quot;<br />
  85                                 Features mark range(s) of residues predicted to be hot loops and
  86                                 annotation row gives raw value for each residue. Values over 0.6
  87                                 indicates hot loop.
  88                         </td>
  89                 </tr>
  90                 <tr>
  91                         <td><strong>REMARK465</strong></td>
  92                         <td>Sequence Feature &amp;<br />Annotation Row
  93                         </td>
  94                         <td>&quot;Missing coordinates in X-ray structure as defined by
  95                                 remark465 entries in PDB. Nonassigned electron densities most often
  96                                 reflect intrinsic disorder, and have been used early on in disorder
  97                                 prediction.&quot;<br /> Features gives range(s) of residues
  98                                 predicted as disordered, and annotation row gives raw value for each
  99                                 residue. Value over 0.1204 indicates disorder.
 100                         </td>
 101                 </tr>
 102         </table>
 103
 104         <p>
 105                 <a name="dsspstates"></a>[1]. DSSP Classification: &alpha;-helix (H),
 106                 310-helix (G), &beta;-strand (E) are ordered, and all other states
 107                 (&beta;-bridge (B), &beta;-turn (T), bend (S), &pi;-helix (I), and
 108                 coil (C)) considered loops or coils.
 109         </p>
 110
 111
 112         <p>
 113                 <strong><a name="ronn"></a><a
 114                         href="http://www.strubi.ox.ac.uk/RONN">RONN</a></strong> <em>a.k.a.</em>
 115                 Regional Order Neural Network<br />This predictor employs an approach
 116                 known as the 'bio-basis' method to predict regions of disorder in
 117                 sequences based on their local similarity with a gold-standard set of
 118                 disordered protein sequences. It yields a set of disorder prediction
 119                 scores, which are shown as sequence annotation below the alignment.
 120         </p>
 121         <table border="1">
 122                 <tr>
 123                         <td><strong>Name</strong></td>
 124                         <td><strong>Annotation type</strong></td>
 125                         <td><strong>Description</strong></td>
 126                 </tr>
 127                 <tr>
 128                         <td><strong>JRonn</strong>[2]</td>
 129                         <td>Annotation Row</td>
 130                         <td>RONN score for each residue in the sequence. Scores above
 131                                 0.5 identify regions of the protein likely to be disordered.</td>
 132                 </tr>
 133         </table>
 134         <p>
 135                 <em>[2]. JRonn denotes the score for this server because JABAWS
 136                         runs a Java port of RONN developed by Peter Troshin and distributed
 137                         as part of <a href="http://www.biojava.org/">Biojava 3</a>
 138                 </em>
 139         </p>
 140         <p>
 141                 <strong><a name="iupred"></a><a
 142                         href="http://iupred.enzim.hu/Help.php">IUPred</a></strong><br /> IUPred
 143                 employs an empirical model to estimate likely regions of disorder.
 144                 There are three different prediction types offered, each using
 145                 different parameters optimized for slightly different applications. It
 146                 provides raw scores based on two models for predicting regions of
 147                 'long disorder' and 'short disorder'. A third predictor identifies
 148                 regions likely to form structured domains.
 149         </p>
 150         <table border="1">
 151                 <tr>
 152                         <td><strong>Name</strong></td>
 153                         <td><strong>Annotation type</strong></td>
 154                         <td><strong>Description</strong></td>
 155                 </tr>
 156                 <tr>
 157                         <td><strong>Long disorder</strong></td>
 158                         <td>Annotation Row</td>
 159                         <td>Prediction of context-independent global disorder that
 160                                 encompasses at least 30 consecutive residues of predicted disorder.
 161                                 Employs a 100 residue window for calculation.<br />Values above 0.5
 162                                 indicates the residue is intrinsically disordered.
 163                         </td>
 164                 </tr>
 165                 <tr>
 166                         <td><strong>Short disorder</strong></td>
 167                         <td>Annotation Row</td>
 168                         <td>Predictor for short, (and probably) context-dependent,
 169                                 disordered regions, such as missing residues in the X-ray structure
 170                                 of an otherwise globular protein. Employs a 25 residue window for
 171                                 calculation, and includes adjustment parameter for chain termini
 172                                 which favors disorder prediction at the ends.<br />Values above 0.5
 173                                 indicate short-range disorder.
 174                         </td>
 175                 </tr>
 176                 <tr>
 177                         <td><strong>Structured domains</strong></td>
 178                         <td>Sequence Feature</td>
 179                         <td>Features highlighting likely globular domains useful for
 180                                 structure genomics investigation. <br />Post-analysis of disordered
 181                                 region profile to find continuous regions confidently predicted to
 182                                 be ordered. Neighbouring regions close to each other are merged,
 183                                 while regions shorter than the minimal domain size of at least 30
 184                                 residues are ignored.
 185                         </td>
 186                 </tr>
 187         </table>
 188         <p>
 189                 <strong><a name="globplot"></a><a
 190                         href="http://globplot.embl.de/">GLOBPLOT</a></strong><br /> Defines regions
 191                 of globularity or natively unstructured regions based on a running sum
 192                 of the propensity of residues to be structured or unstructured. The
 193                 propensity is calculated based on the probability of each amino acid
 194                 being observed within well defined regions of secondary structure or
 195                 within regions of random coil. The initial signal is smoothed with a
 196                 Savitzky-Golay filter, and its first order derivative computed.
 197                 Residues for which the first order derivative is positive are
 198                 designated as natively unstructured, whereas those with negative
 199                 values are structured.<br />
 200         <table border="1">
 201                 <tr>
 202                         <td><strong>Name</strong></td>
 203                         <td><strong>Annotation type</strong></td>
 204                         <td><strong>Description</strong></td>
 205                 </tr>
 206                 <tr>
 207                         <td><strong>Disordered Region</strong></td>
 208                         <td>Sequence Feature</td>
 209                         <td><br />Sequence features marking range(s) of residues with
 210                                 positive dydx values (correspond to the #Disorder column from JABAWS
 211                                 results)</td>
 212                 </tr>
 213                 <tr>
 214                         <td><strong>Globular Domain</strong>
 215                         <td>Sequence Feature</td>
 216                         <td>Putative globular domains</td>
 217                 </tr>
 218                 <tr>
 219                         <td><strong>Dydx</strong></td>
 220                         <td>Annotation row</td>
 221                         <td>First order derivative of smoothed score. Values above 0
 222                                 indicates residue is disordered.</td>
 223                 </tr>
 224                 <tr>
 225                         <td><strong>Smoothed Score<br />Raw Score
 226                         </strong></td>
 227                         <td>Annotation Row</td>
 228                         <td>The smoothed and raw scores used to create the differential
 229                                 signal that indicates the presence of unstructured regions.<br /> <em>These
 230                                         are hidden by default, but can be shown by right-clicking on the
 231                                         alignment annotation panel and selecting <strong>Show
 232                                                 hidden annotation</strong>
 233                         </em>
 234                         </td>
 235                 </tr>
 236         </table>
 237         <p>
 238                 <em>Documentation and thresholds for the JABAWS Disorder
 239                         predictors adapted from a personal communication by Nancy Giang,
 240                         2012.</em>
 241         </p>
 242 </body>
 243 </html>