3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
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20 <title>JABAWS Protein Disorder Prediction Services</title>
24 <strong>JABAWS Protein Disorder Prediction Services</strong> <br />
25 The <strong>Web Services→Disorder</strong> menu in the alignment
26 window allows access to protein disorder prediction services provided
27 by the configured <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS
28 servers</a>. Each service operates on sequences in the alignment to
29 identify regions likely to be unstructured or flexible, or
30 alternately, fold to form globular domains.
33 Predictor results include both <a href="../features/seqfeatures.html">sequence
34 features</a> and sequence associated <a
35 href="../features/annotation.html">alignment annotation</a> rows.
36 Features display is controlled from the <a
37 href="../features/featureSettings.html">Feature Settings</a> dialog
38 box. Clicking on the ID for a disorder prediction annotation row will
39 highlight or select (if double clicked) the associated sequence for
40 that row. You can also use the <em>Sequence Associated</em> option in
41 the <a href="../colourSchemes/annotationColouring.html">Colour By
42 Annotation</a> dialog box to colour sequences according to the results of
43 predictors shown as annotation rows.
45 <p>JABAWS 2.0 provides four disorder predictors which are described
48 <li><a href="#disembl">DisEMBL</a></li>
49 <li><a href="#iupred">IUPred</a></li>
50 <li><a href="#ronn">RONN</a></li>
51 <li><a href="#globplot">GlobPlot</a></li>
54 <strong><a name="disembl"></a><a href="http://dis.embl.de/">DisEMBL
55 (Linding et al., 2003)</a> </strong> <br /> DisEMBL is a set of machine-learning
56 based predictors trained to recognise disorder-related annotation
57 found on PDB structures.
61 <td><strong>Name</strong></td>
62 <td><strong>Annotation type</strong></td>
63 <td><strong>Description</strong></td>
66 <td><strong>COILS</strong></td>
67 <td>Sequence Feature &<br />Annotation Row
69 <td>Predicts loops/coils according to DSSP definition<a
70 href="#dsspstates">[1]</a>.<br />Features mark range(s) of residues
71 predicted as loops/coils, and annotation row gives raw value for
72 each residue. Value over 0.516 indicates loop/coil.
76 <td><strong>HOTLOOPS</strong></td>
77 <td>Sequence Feature &<br />Annotation Row
79 <td>"Hot loops constitute a refined subset of <strong>COILS</strong>,
80 namely those loops with a high degree of mobility as determined from
81 Cα temperature factors (B factors). It follows that highly
82 dynamic loops should be considered protein disorder."<br />
83 Features mark range(s) of residues predicted to be hot loops and
84 annotation row gives raw value for each residue. Values over 0.6
89 <td><strong>REMARK465</strong></td>
90 <td>Sequence Feature &<br />Annotation Row
92 <td>"Missing coordinates in X-ray structure as defined by
93 remark465 entries in PDB. Nonassigned electron densities most often
94 reflect intrinsic disorder, and have been used early on in disorder
95 prediction."<br /> Features gives range(s) of residues
96 predicted as disordered, and annotation row gives raw value for each
97 residue. Value over 0.1204 indicates disorder.
103 <a name="dsspstates"></a>[1]. DSSP Classification: α-helix (H),
104 310-helix (G), β-strand (E) are ordered, and all other states
105 (β-bridge (B), β-turn (T), bend (S), π-helix (I), and
106 coil (C)) considered loops or coils.
111 <strong><a name="ronn"></a><a
112 href="http://www.strubi.ox.ac.uk/RONN">RONN</a></strong> <em>a.k.a.</em>
113 Regional Order Neural Network<br />This predictor employs an approach
114 known as the 'bio-basis' method to predict regions of disorder in
115 sequences based on their local similarity with a gold-standard set of
116 disordered protein sequences. It yields a set of disorder prediction
117 scores, which are shown as sequence annotation below the alignment.
121 <td><strong>Name</strong></td>
122 <td><strong>Annotation type</strong></td>
123 <td><strong>Description</strong></td>
126 <td><strong>JRonn</strong>[2]</td>
127 <td>Annotation Row</td>
128 <td>RONN score for each residue in the sequence. Scores above
129 0.5 identify regions of the protein likely to be disordered.</td>
133 <em>[2]. JRonn denotes the score for this server because JABAWS
134 runs a Java port of RONN developed by Peter Troshin and distributed
135 as part of <a href="http://www.biojava.org/">Biojava 3</a>
139 <strong><a name="iupred"></a><a
140 href="http://iupred.enzim.hu/Help.php">IUPred</a></strong><br /> IUPred
141 employs an empirical model to estimate likely regions of disorder.
142 There are three different prediction types offered, each using
143 different parameters optimized for slightly different applications. It
144 provides raw scores based on two models for predicting regions of
145 'long disorder' and 'short disorder'. A third predictor identifies
146 regions likely to form structured domains.
150 <td><strong>Name</strong></td>
151 <td><strong>Annotation type</strong></td>
152 <td><strong>Description</strong></td>
155 <td><strong>Long disorder</strong></td>
156 <td>Annotation Row</td>
157 <td>Prediction of context-independent global disorder that
158 encompasses at least 30 consecutive residues of predicted disorder.
159 Employs a 100 residue window for calculation.<br />Values above 0.5
160 indicates the residue is intrinsically disordered.
164 <td><strong>Short disorder</strong></td>
165 <td>Annotation Row</td>
166 <td>Predictor for short, (and probably) context-dependent,
167 disordered regions, such as missing residues in the X-ray structure
168 of an otherwise globular protein. Employs a 25 residue window for
169 calculation, and includes adjustment parameter for chain termini
170 which favors disorder prediction at the ends.<br />Values above 0.5
171 indicate short-range disorder.
175 <td><strong>Structured domains</strong></td>
176 <td>Sequence Feature</td>
177 <td>Features highlighting likely globular domains useful for
178 structure genomics investigation. <br />Post-analysis of disordered
179 region profile to find continuous regions confidently predicted to
180 be ordered. Neighbouring regions close to each other are merged,
181 while regions shorter than the minimal domain size of at least 30
182 residues are ignored.
187 <strong><a name="globplot"></a><a
188 href="http://globplot.embl.de/">GLOBPLOT</a></strong><br /> Defines regions
189 of globularity or natively unstructured regions based on a running sum
190 of the propensity of residues to be structured or unstructured. The
191 propensity is calculated based on the probability of each amino acid
192 being observed within well defined regions of secondary structure or
193 within regions of random coil. The initial signal is smoothed with a
194 Savitzky-Golay filter, and its first order derivative computed.
195 Residues for which the first order derivative is positive are
196 designated as natively unstructured, whereas those with negative
197 values are structured.<br />
200 <td><strong>Name</strong></td>
201 <td><strong>Annotation type</strong></td>
202 <td><strong>Description</strong></td>
205 <td><strong>Disordered Region</strong></td>
206 <td>Sequence Feature</td>
207 <td><br />Sequence features marking range(s) of residues with
208 positive dydx values (correspond to the #Disorder column from JABAWS
212 <td><strong>Globular Domain</strong>
213 <td>Sequence Feature</td>
214 <td>Putative globular domains</td>
217 <td><strong>Dydx</strong></td>
218 <td>Annotation row</td>
219 <td>First order derivative of smoothed score. Values above 0
220 indicates residue is disordered.</td>
223 <td><strong>Smoothed Score<br />Raw Score
225 <td>Annotation Row</td>
226 <td>The smoothed and raw scores used to create the differential
227 signal that indicates the presence of unstructured regions.<br /> <em>These
228 are hidden by default, but can be shown by right-clicking on the
229 alignment annotation panel and selecting <strong>Show
230 hidden annotation</strong>
236 <em>Documentation and thresholds for the JABAWS Disorder
237 predictors adapted from a personal communication by Nancy Giang,