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<h1>BioJava Webservices</h1>

<p>

<a href="http://biojava.org">BioJava</a> is a powerful library of

bioinformatics tools, but leveraging BioJava from web interfaces is

challenging. This provides a number of APIs and pre-build interfaces

for accessing BioJava through the browser.

</p>

<h2>biojava-structure</h2>

<p>

BioJava understands and can automatically fetch a wide variety of

structure formats. In the following examples,

<tt>:id</tt>

can be replaced by any of the following:

<ul>

<li><b>PDB</b> PDB identifier, optionally followed by chain

and/or residue ranges. Examples: 4hhb, 4hhb.A, 4hhb.A:1-50.</li>

<li><b>SCOP</b> SCOPe domain. Example: d1h6w.2</li>

<li><b>PDP</b> Protein Domain Parser domain. Example: PDP:4HHBAa</li>

<li><b>CATH</b> Cath domains. Example: 1qvrC03</li>

<li><b>ECOD</b> ECOD domain. Example: e1lyw.1

<li><b>BIO</b> Biological assembly. Example: BIO:2ehz:1</li>

</ul>

</p>

<h3>Fetching structures</h3>

<p>

<table class="route">

<tr>

<td><pre>/pdb/:id</pre></td>

<td>Example: <a href="/pdb/1itb.A">/pdb/1itb.A</a></td>

</tr>

<tr>

<td><pre>/mmcif/:id</pre></td>

<td>Example: <a href="/mmcif/1itb.A">/mmcif/1itb.A</a></td>

</tr>

<tr>

<td><pre>/mmtf/:id</pre></td>

<td>Example: <a href="/mmtf/1itb.A">/mmtf/1itb.A</a></td>

</tr>

</table>

Returns the requested structure in

<a href="http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html">PDB</a>/

<a href="http://mmcif.wwpdb.org/">mmCIF</a>/<a href="http://mmtf.rcsb.org/">MMTF</a> format.

</p>

<h3>Viewing structures</h3>

<p>

<table class="route">

<tr>

<td><pre>/ngl/:id</pre></td>

<td>Example: <a href="/ngl/1itb.A">/ngl/1itb.A</a></td>

</tr>

</table>

Views the requested structure using <a

href="https://github.com/arose/ngl">NGL</a>.

</p>

<h3>CE-Symm</h3>

<p>

<table class="route">

<tr>

<td><pre>/cesymm/:id</pre></td>

<td>Example: <a href="/cesymm/1itb.A">/cesymm/1itb.A</a></td>

</tr>

</table>

Analyze the structure for internal symmetry using <a

href="https://github.com/rcsb/symmetry">CE-Symm</a>.

</p>

<p>

<table class="route">

<tr>

<td><pre>/cesymm/:id/multi</pre></td>

<td>Example: <a href="/cesymm/1itb.A/multi">/cesymm/1itb.A/multi</a></td>

</tr>

</table>

View the CE-Symm alignment as a multiple structure superposition.

</p>

<p>Information about the alignment is available in several

formats:

<table class="route">

<tr>

<td><pre>/cesymm/:id/pdb</pre></td>

<td>Example: <a href="/cesymm/1itb.A/pdb">/cesymm/1itb.A/pdb</a></td>

</tr>

</table>

PDB file with a superposition of the structure.

<table class="route">

<tr>

<td><pre>/cesymm/:id/mmtf</pre></td>

<td>Example: <a href="/cesymm/1itb.A/mmtf">/cesymm/1itb.A/mmtf</a></td>

</tr>

</table>

MMTF file with a superposition of the structure.

<table class="route">

<tr>

<td><pre>/cesymm/:id/json</pre></td>

<td>Example: <a href="/cesymm/1itb.A/json">/cesymm/1itb.A/json</a></td>

</tr>

</table>

JSON describing the alignment.

<table class="route">

<tr>

<td><pre>/cesymm/:id/tsv</pre></td>

<td>Example: <a href="/cesymm/1itb.A/tsv">/cesymm/1itb.A/tsv</a></td>

</tr>

</table>

All aligned residues in the alignment, in tsv format.

<table class="route">

<tr>

<td><pre>/cesymm/:id/fasta</pre></td>

<td>Example: <a href="/cesymm/1itb.A/fasta">/cesymm/1itb.A/fasta</a></td>

</tr>

</table>

FASTA format multiple alignment of all repeats. Upper-case letters are aligned.

Lower case letters and hyphens are gaps.

</p>

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