help/html/webServices/proteinDisorder.html

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