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-<head>
-<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 2.2 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>
- <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/">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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