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21 <title>JABAWS Protein Disorder Prediction Services</title>
25 <strong>JABAWS Protein Disorder Prediction Services</strong> <br />
26 The <strong>Web Services→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.
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.
46 <p>JABAWS 2.0 provides four disorder predictors which are described
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>
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.
62 <td><strong>Name</strong></td>
63 <td><strong>Annotation type</strong></td>
64 <td><strong>Description</strong></td>
67 <td><strong>COILS</strong></td>
68 <td>Sequence Feature &<br />Annotation Row
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.
77 <td><strong>HOTLOOPS</strong></td>
78 <td>Sequence Feature &<br />Annotation Row
80 <td>"Hot loops constitute a refined subset of <strong>COILS</strong>,
81 namely those loops with a high degree of mobility as determined from
82 Cα temperature factors (B factors). It follows that highly
83 dynamic loops should be considered protein disorder."<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
90 <td><strong>REMARK465</strong></td>
91 <td>Sequence Feature &<br />Annotation Row
93 <td>"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."<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.
104 <a name="dsspstates"></a>[1]. DSSP Classification: α-helix (H),
105 310-helix (G), β-strand (E) are ordered, and all other states
106 (β-bridge (B), β-turn (T), bend (S), π-helix (I), and
107 coil (C)) considered loops or coils.
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.
122 <td><strong>Name</strong></td>
123 <td><strong>Annotation type</strong></td>
124 <td><strong>Description</strong></td>
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>
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>
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.
151 <td><strong>Name</strong></td>
152 <td><strong>Annotation type</strong></td>
153 <td><strong>Description</strong></td>
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.
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.
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.
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 />
201 <td><strong>Name</strong></td>
202 <td><strong>Annotation type</strong></td>
203 <td><strong>Description</strong></td>
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
213 <td><strong>Globular Domain</strong>
214 <td>Sequence Feature</td>
215 <td>Putative globular domains</td>
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>
224 <td><strong>Smoothed Score<br />Raw Score
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>
237 <em>Documentation and thresholds for the JABAWS Disorder
238 predictors adapted from a personal communication by Nancy Giang,