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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 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.
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.
47 <p>JABAWS 2.0 provides four disorder predictors which are described
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>
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.
63 <td><strong>Name</strong></td>
64 <td><strong>Annotation type</strong></td>
65 <td><strong>Description</strong></td>
68 <td><strong>COILS</strong></td>
69 <td>Sequence Feature &<br />Annotation Row
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.
78 <td><strong>HOTLOOPS</strong></td>
79 <td>Sequence Feature &<br />Annotation Row
81 <td>"Hot loops constitute a refined subset of <strong>COILS</strong>,
82 namely those loops with a high degree of mobility as determined from
83 Cα temperature factors (B factors). It follows that highly
84 dynamic loops should be considered protein disorder."<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
91 <td><strong>REMARK465</strong></td>
92 <td>Sequence Feature &<br />Annotation Row
94 <td>"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."<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.
105 <a name="dsspstates"></a>[1]. DSSP Classification: α-helix (H),
106 310-helix (G), β-strand (E) are ordered, and all other states
107 (β-bridge (B), β-turn (T), bend (S), π-helix (I), and
108 coil (C)) considered loops or coils.
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.
123 <td><strong>Name</strong></td>
124 <td><strong>Annotation type</strong></td>
125 <td><strong>Description</strong></td>
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>
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>
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.
152 <td><strong>Name</strong></td>
153 <td><strong>Annotation type</strong></td>
154 <td><strong>Description</strong></td>
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.
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.
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.
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 />
202 <td><strong>Name</strong></td>
203 <td><strong>Annotation type</strong></td>
204 <td><strong>Description</strong></td>
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
214 <td><strong>Globular Domain</strong>
215 <td>Sequence Feature</td>
216 <td>Putative globular domains</td>
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>
225 <td><strong>Smoothed Score<br />Raw Score
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>
238 <em>Documentation and thresholds for the JABAWS Disorder
239 predictors adapted from a personal communication by Nancy Giang,