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<title>JABAWS Protein Disorder Prediction Services</title>
</head>
<body>
- <p>
- <strong>JABAWS Protein Disorder Prediction Services</strong> <br />
- The <strong>Web Services→Disorder</strong> menu in the alignment
- window allows access to protein disorder prediction services provided
- by the configured <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS
- servers</a>. Each service operates on sequences in the alignment or
- currently selected region (<em>since Jalview 2.8.0b1</em>) to identify
- regions likely to be unstructured or flexible, or alternately, fold to
- form globular domains.
- </p>
- <p>
- Predictor results include both <a href="../features/seqfeatures.html">sequence
- features</a> and sequence associated <a
- href="../features/annotation.html">alignment annotation</a> rows.
- Features display is controlled from the <a
- href="../features/featureSettings.html">Feature Settings</a> dialog
- box. Clicking on the ID for a disorder prediction annotation row will
- highlight or select (if double clicked) the associated sequence for
- that row. You can also use the <em>Sequence Associated</em> option in
- the <a href="../colourSchemes/annotationColouring.html">Colour By
- Annotation</a> dialog box to colour sequences according to the results of
- predictors shown as annotation rows.
- </p>
- <p>JABAWS 2.0 provides four disorder predictors which are described
- below:</p>
- <ul>
- <li><a href="#disembl">DisEMBL</a></li>
- <li><a href="#iupred">IUPred</a></li>
- <li><a href="#ronn">RONN</a></li>
- <li><a href="#globplot">GlobPlot</a></li>
- </ul>
- <p>
- <strong><a name="disembl"></a><a href="http://dis.embl.de/">DisEMBL
- (Linding et al., 2003)</a> </strong> <br /> DisEMBL is a set of machine-learning
- based predictors trained to recognise disorder-related annotation
- found on PDB structures.
- </p>
- <table border="1">
- <tr>
- <td><strong>Name</strong></td>
- <td><strong>Annotation type</strong></td>
- <td><strong>Description</strong></td>
- </tr>
- <tr>
- <td><strong>COILS</strong></td>
- <td>Sequence Feature &<br />Annotation Row
- </td>
- <td>Predicts loops/coils according to DSSP definition<a
- href="#dsspstates">[1]</a>.<br />Features mark range(s) of residues
- predicted as loops/coils, and annotation row gives raw value for
- each residue. Value over 0.516 indicates loop/coil.
- </td>
- </tr>
- <tr>
- <td><strong>HOTLOOPS</strong></td>
- <td>Sequence Feature &<br />Annotation Row
- </td>
- <td>"Hot loops constitute a refined subset of <strong>COILS</strong>,
- namely those loops with a high degree of mobility as determined from
- Cα temperature factors (B factors). It follows that highly
- dynamic loops should be considered protein disorder."<br />
- Features mark range(s) of residues predicted to be hot loops and
- annotation row gives raw value for each residue. Values over 0.6
- indicates hot loop.
- </td>
- </tr>
- <tr>
- <td><strong>REMARK465</strong></td>
- <td>Sequence Feature &<br />Annotation Row
- </td>
- <td>"Missing coordinates in X-ray structure as defined by
- remark465 entries in PDB. Nonassigned electron densities most often
- reflect intrinsic disorder, and have been used early on in disorder
- prediction."<br /> Features gives range(s) of residues
- predicted as disordered, and annotation row gives raw value for each
- residue. Value over 0.1204 indicates disorder.
- </td>
- </tr>
- </table>
+ <p>
+ <strong>JABAWS Protein Disorder Prediction Services</strong> <br />
+ The <strong>Web Services→Disorder</strong> menu in the
+ alignment window allows access to protein disorder prediction
+ services provided by the configured <a
+ href="http://www.compbio.dundee.ac.uk/jabaws"
+ >JABAWS servers</a>. Each service operates on sequences in the
+ alignment or currently selected region (<em>since Jalview
+ 2.8.0b1</em>) to identify regions likely to be unstructured or
+ flexible, or alternately, fold to form globular domains.
+ </p>
+ <p>
+ Predictor results include both <a
+ href="../features/seqfeatures.html"
+ >sequence features</a> and sequence associated <a
+ href="../features/annotation.html"
+ >alignment annotation</a> rows. Features display is controlled from
+ the <a href="../features/featureSettings.html">Feature Settings</a>
+ dialog box. Clicking on the ID for a disorder prediction annotation
+ row will highlight or select (if double clicked) the associated
+ sequence for that row. You can also use the <em>Sequence
+ Associated</em> option in the <a
+ href="../colourSchemes/annotationColouring.html"
+ >Colour By Annotation</a> dialog box to colour sequences according to
+ the results of predictors shown as annotation rows.
+ </p>
+ <p>JABAWS 2.0 provides four disorder predictors which are
+ described below:</p>
+ <ul>
+ <li><a href="#disembl">DisEMBL</a></li>
+ <li><a href="#iupred">IUPred</a></li>
+ <li><a href="#ronn">RONN</a></li>
+ <li><a href="#globplot">GlobPlot</a></li>
+ </ul>
+ <p>
+ <strong><a name="disembl"></a><a href="http://dis.embl.de/">DisEMBL
+ (Linding et al., 2003)</a> </strong> <br /> DisEMBL is a set of
+ machine-learning based predictors trained to recognise
+ disorder-related annotation found on PDB structures.
+ </p>
+ <table border="1">
+ <tr>
+ <td><strong>Name</strong></td>
+ <td><strong>Annotation type</strong></td>
+ <td><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td><strong>COILS</strong></td>
+ <td>Sequence Feature &<br />Annotation Row
+ </td>
+ <td>Predicts loops/coils according to DSSP definition<a
+ href="#dsspstates"
+ >[1]</a>.<br />Features mark range(s) of residues predicted as
+ loops/coils, and annotation row gives raw value for each
+ residue. Value over 0.516 indicates loop/coil.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>HOTLOOPS</strong></td>
+ <td>Sequence Feature &<br />Annotation Row
+ </td>
+ <td>"Hot loops constitute a refined subset of <strong>COILS</strong>,
+ namely those loops with a high degree of mobility as determined
+ from Cα temperature factors (B factors). It follows that
+ highly dynamic loops should be considered protein
+ disorder."<br /> Features mark range(s) of residues
+ predicted to be hot loops and annotation row gives raw value for
+ each residue. Values over 0.6 indicates hot loop.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>REMARK465</strong></td>
+ <td>Sequence Feature &<br />Annotation Row
+ </td>
+ <td>"Missing coordinates in X-ray structure as defined
+ by remark465 entries in PDB. Nonassigned electron densities most
+ often reflect intrinsic disorder, and have been used early on in
+ disorder prediction."<br /> Features gives range(s) of
+ residues predicted as disordered, and annotation row gives raw
+ value for each residue. Value over 0.1204 indicates disorder.
+ </td>
+ </tr>
+ </table>
- <p>
- <a name="dsspstates"></a>[1]. DSSP Classification: α-helix (H),
- 310-helix (G), β-strand (E) are ordered, and all other states
- (β-bridge (B), β-turn (T), bend (S), π-helix (I), and
- coil (C)) considered loops or coils.
- </p>
+ <p>
+ <a name="dsspstates"></a>[1]. DSSP Classification: α-helix
+ (H), 310-helix (G), β-strand (E) are ordered, and all other
+ states (β-bridge (B), β-turn (T), bend (S), π-helix
+ (I), and coil (C)) considered loops or coils.
+ </p>
- <p>
- <strong><a name="ronn"></a><a
- href="http://www.strubi.ox.ac.uk/RONN">RONN</a></strong> <em>a.k.a.</em>
- Regional Order Neural Network<br />This predictor employs an approach
- known as the 'bio-basis' method to predict regions of disorder in
- sequences based on their local similarity with a gold-standard set of
- disordered protein sequences. It yields a set of disorder prediction
- scores, which are shown as sequence annotation below the alignment.
- </p>
- <table border="1">
- <tr>
- <td><strong>Name</strong></td>
- <td><strong>Annotation type</strong></td>
- <td><strong>Description</strong></td>
- </tr>
- <tr>
- <td><strong>JRonn</strong>[2]</td>
- <td>Annotation Row</td>
- <td>RONN score for each residue in the sequence. Scores above
- 0.5 identify regions of the protein likely to be disordered.</td>
- </tr>
- </table>
- <p>
- <em>[2]. JRonn denotes the score for this server because JABAWS
- runs a Java port of RONN developed by Peter Troshin and distributed
- as part of <a href="http://www.biojava.org/">Biojava 3</a>
- </em>
- </p>
- <p>
- <strong><a name="iupred"></a><a
- href="http://iupred.enzim.hu/Help.php">IUPred</a></strong><br /> IUPred
- employs an empirical model to estimate likely regions of disorder.
- There are three different prediction types offered, each using
- different parameters optimized for slightly different applications. It
- provides raw scores based on two models for predicting regions of
- 'long disorder' and 'short disorder'. A third predictor identifies
- regions likely to form structured domains.
- </p>
- <table border="1">
- <tr>
- <td><strong>Name</strong></td>
- <td><strong>Annotation type</strong></td>
- <td><strong>Description</strong></td>
- </tr>
- <tr>
- <td><strong>Long disorder</strong></td>
- <td>Annotation Row</td>
- <td>Prediction of context-independent global disorder that
- encompasses at least 30 consecutive residues of predicted disorder.
- Employs a 100 residue window for calculation.<br />Values above 0.5
- indicates the residue is intrinsically disordered.
- </td>
- </tr>
- <tr>
- <td><strong>Short disorder</strong></td>
- <td>Annotation Row</td>
- <td>Predictor for short, (and probably) context-dependent,
- disordered regions, such as missing residues in the X-ray structure
- of an otherwise globular protein. Employs a 25 residue window for
- calculation, and includes adjustment parameter for chain termini
- which favors disorder prediction at the ends.<br />Values above 0.5
- indicate short-range disorder.
- </td>
- </tr>
- <tr>
- <td><strong>Structured domains</strong></td>
- <td>Sequence Feature</td>
- <td>Features highlighting likely globular domains useful for
- structure genomics investigation. <br />Post-analysis of disordered
- region profile to find continuous regions confidently predicted to
- be ordered. Neighbouring regions close to each other are merged,
- while regions shorter than the minimal domain size of at least 30
- residues are ignored.
- </td>
- </tr>
- </table>
- <p>
- <strong><a name="globplot"></a><a
- href="http://globplot.embl.de/">GLOBPLOT</a></strong><br /> Defines regions
- of globularity or natively unstructured regions based on a running sum
- of the propensity of residues to be structured or unstructured. The
- propensity is calculated based on the probability of each amino acid
- being observed within well defined regions of secondary structure or
- within regions of random coil. The initial signal is smoothed with a
- Savitzky-Golay filter, and its first order derivative computed.
- Residues for which the first order derivative is positive are
- designated as natively unstructured, whereas those with negative
- values are structured.<br />
- <table border="1">
- <tr>
- <td><strong>Name</strong></td>
- <td><strong>Annotation type</strong></td>
- <td><strong>Description</strong></td>
- </tr>
- <tr>
- <td><strong>Disordered Region</strong></td>
- <td>Sequence Feature</td>
- <td><br />Sequence features marking range(s) of residues with
- positive dydx values (correspond to the #Disorder column from JABAWS
- results)</td>
- </tr>
- <tr>
- <td><strong>Globular Domain</strong>
- <td>Sequence Feature</td>
- <td>Putative globular domains</td>
- </tr>
- <tr>
- <td><strong>Dydx</strong></td>
- <td>Annotation row</td>
- <td>First order derivative of smoothed score. Values above 0
- indicates residue is disordered.</td>
- </tr>
- <tr>
- <td><strong>Smoothed Score<br />Raw Score
- </strong></td>
- <td>Annotation Row</td>
- <td>The smoothed and raw scores used to create the differential
- signal that indicates the presence of unstructured regions.<br /> <em>These
- are hidden by default, but can be shown by right-clicking on the
- alignment annotation panel and selecting <strong>Show
- hidden annotation</strong>
- </em>
- </td>
- </tr>
- </table>
- <p>
- <em>Documentation and thresholds for the JABAWS Disorder
- predictors adapted from a personal communication by Nancy Giang,
- 2012.</em>
- </p>
+ <p>
+ <strong><a name="ronn"></a><a
+ href="http://www.strubi.ox.ac.uk/RONN"
+ >RONN</a></strong> <em>a.k.a.</em> Regional Order Neural Network<br />This
+ predictor employs an approach known as the 'bio-basis' method to
+ predict regions of disorder in sequences based on their local
+ similarity with a gold-standard set of disordered protein sequences.
+ It yields a set of disorder prediction scores, which are shown as
+ sequence annotation below the alignment.
+ </p>
+ <table border="1">
+ <tr>
+ <td><strong>Name</strong></td>
+ <td><strong>Annotation type</strong></td>
+ <td><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td><strong>JRonn</strong>[2]</td>
+ <td>Annotation Row</td>
+ <td>RONN score for each residue in the sequence. Scores above
+ 0.5 identify regions of the protein likely to be disordered.</td>
+ </tr>
+ </table>
+ <p>
+ <em>[2]. JRonn denotes the score for this server because JABAWS
+ runs a Java port of RONN developed by Peter Troshin and
+ distributed as part of <a href="http://www.biojava.org/">Biojava
+ 3</a>
+ </em>
+ </p>
+ <p>
+ <strong><a name="iupred"></a><a
+ href="http://iupred.enzim.hu/Help.php"
+ >IUPred</a></strong><br /> IUPred employs an empirical model to estimate
+ likely regions of disorder. There are three different prediction
+ types offered, each using different parameters optimized for
+ slightly different applications. It provides raw scores based on two
+ models for predicting regions of 'long disorder' and 'short
+ disorder'. A third predictor identifies regions likely to form
+ structured domains.
+ </p>
+ <table border="1">
+ <tr>
+ <td><strong>Name</strong></td>
+ <td><strong>Annotation type</strong></td>
+ <td><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td><strong>Long disorder</strong></td>
+ <td>Annotation Row</td>
+ <td>Prediction of context-independent global disorder that
+ encompasses at least 30 consecutive residues of predicted
+ disorder. Employs a 100 residue window for calculation.<br />Values
+ above 0.5 indicates the residue is intrinsically disordered.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>Short disorder</strong></td>
+ <td>Annotation Row</td>
+ <td>Predictor for short, (and probably) context-dependent,
+ disordered regions, such as missing residues in the X-ray
+ structure of an otherwise globular protein. Employs a 25 residue
+ window for calculation, and includes adjustment parameter for
+ chain termini which favors disorder prediction at the ends.<br />Values
+ above 0.5 indicate short-range disorder.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>Structured domains</strong></td>
+ <td>Sequence Feature</td>
+ <td>Features highlighting likely globular domains useful for
+ structure genomics investigation. <br />Post-analysis of
+ disordered region profile to find continuous regions confidently
+ predicted to be ordered. Neighbouring regions close to each
+ other are merged, while regions shorter than the minimal domain
+ size of at least 30 residues are ignored.
+ </td>
+ </tr>
+ </table>
+ <p>
+ <strong><a name="globplot"></a><a
+ href="http://globplot.embl.de/"
+ >GLOBPLOT</a></strong><br /> Defines regions of globularity or natively
+ unstructured regions based on a running sum of the propensity of
+ residues to be structured or unstructured. The propensity is
+ calculated based on the probability of each amino acid being
+ observed within well defined regions of secondary structure or
+ within regions of random coil. The initial signal is smoothed with a
+ Savitzky-Golay filter, and its first order derivative computed.
+ Residues for which the first order derivative is positive are
+ designated as natively unstructured, whereas those with negative
+ values are structured.<br />
+ <table border="1">
+ <tr>
+ <td><strong>Name</strong></td>
+ <td><strong>Annotation type</strong></td>
+ <td><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td><strong>Disordered Region</strong></td>
+ <td>Sequence Feature</td>
+ <td><br />Sequence features marking range(s) of residues
+ with positive dydx values (correspond to the #Disorder column
+ from JABAWS results)</td>
+ </tr>
+ <tr>
+ <td><strong>Globular Domain</strong>
+ <td>Sequence Feature</td>
+ <td>Putative globular domains</td>
+ </tr>
+ <tr>
+ <td><strong>Dydx</strong></td>
+ <td>Annotation row</td>
+ <td>First order derivative of smoothed score. Values above 0
+ indicates residue is disordered.</td>
+ </tr>
+ <tr>
+ <td><strong>Smoothed Score<br />Raw Score
+ </strong></td>
+ <td>Annotation Row</td>
+ <td>The smoothed and raw scores used to create the
+ differential signal that indicates the presence of unstructured
+ regions.<br /> <em>These are hidden by default, but can be
+ shown by right-clicking on the alignment annotation panel and
+ selecting <strong>Show hidden annotation</strong>
+ </em>
+ </td>
+ </tr>
+ </table>
+ <p>
+ <em>Documentation and thresholds for the JABAWS Disorder
+ predictors adapted from a personal communication by Nancy Giang,
+ 2012.</em>
+ </p>
</body>
</html>
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