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