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<h2 class="text-uppercase">
CD-Code
</h2>
<p>
CD-CODE is a comprehensive, manually curated database for
<a
href="https://wiki.ddcode.org/Membraneless_compartments"
class="color-accent-color"
>biomolecular condensates</a> and their constituents as well as
an <a
href="https://wiki.ddcode.org/"
class="color-accent-color"
>encyclopedia</a> for the scientific terms used to describe
them. Biomolecular condensates are cellular structures that are formed by
<a
href="https://wiki.ddcode.org/Membraneless_compartments"
class="color-accent-color"
>phase separation</a>. In cells, phase separation is driven by <a
href="https://wiki.ddcode.org/Scaffolds_and_Clients"
class="color-accent-color"
>driver</a>
proteins/nucleic acid, which in turn recruit <a
href="https://wiki.ddcode.org/Scaffolds_and_Clients"
class="color-accent-color"
>client</a> molecules into the
condensate. It is important to note that a particular protein/nucleic acid
may be a driver in one condensate but the client in another. Moreover, the
formation of condensates might be regulated by <a
href="https://wiki.ddcode.org/Scaffolds_and_Clients"
class="color-accent-color"
>regulator</a> proteins through
specific biochemical activities, but they do not necessarily need to be a
part of the condensate.
</p>
<p>
CD-CODE is aimed at becoming a valuable resource for the phase separation
and condensate community by providing 1) a reliable literature mined
database on all biomolecular condensates and their constituents; 2) an
encyclopedia and ontology of the scientific terms and definitions used in
the field of phase separation and condensate biology and 3) a standardised
list of terminologyes in the field. All data here are manually curated and
experimental details and references are provided; this provides the basis
of our scoring system.
</p>
<p>
Protein definition: Proteins on CD-CODE are divided three groups.
</p>
<p>
<b>Drivers:</b> Proteins which have at least one of the following features.
<ul class="list-decimal list-inside px-8">
<li
v-for="items in driversList"
:key="items"
>
{{ items }}
</li>
</ul>
</p>
<p>
<b>Clients:</b> Proteins which are part of a condensate, but driven into it by driver proteins.
</p>
<p>
<b>Regulators:</b> Proteins which biochemically/enzymatically regulate the formation of a condensate, but are structurally not part of it.
</p>
<p>
<b>Scoring system on CD-CODE:</b> At CD-CODE is having three-fold scoring system (evidence stars)
<ol class="list-decimal list-inside px-8">
<li
v-for="items in scoringSysList"
:key="items"
>
{{ items }}
</li>
</ol>
</p>
<div>
<p class="underline">
Evidence of a protein being in a condensate:
</p>
<p>
CD-CODE initially started off as an aggregation of
existing protein-phase-separation databases namely - <a
href="http://llps.biocuckoo.cn/"
class="color-accent-color"
>http://llps.biocuckoo.cn/</a> (dr_llps), <a
href="http://bio-comp.org.cn/llpsdb/home.html "
class="color-accent-color"
>http://bio-comp.org.cn/llpsdb/home.html </a> (llps_db), <a
href="http://db.phasep.pro/"
class="color-accent-color"
>http://db.phasep.pro/</a> (phase_pro) and <a
href="https://phasepro.elte.hu/"
class="color-accent-color"
/> (phase_hu). Within these four source databases, we were also able to find publications (via text mining) stating localization of these phase-separating proteins into biomolecular condensates.
</p>
</div>
<div>
<p>
Using the above two datapoints (source database annotations and publications), we devised a rule-based mechanism to rate the evidence of a protein being a condensate, which goes as follow:
<ul class="list-disc list-inside px-8">
<li
v-for="items in evidenceProteinRateList"
:key="items"
v-html="items"
/>
</ul>
</p>
<p>
Besides these initial ratings, it is also possible for a contributor to modify these ratings.
</p>
</div>
<div>
<p class="undeline">
Evidence of the existence of a condensate along with its proteome:
</p>
<p>
Using the above ratings of a protein existing in a condensate, and computing the median of these scores, we provide a rating to the existence of the condensate as a whole.
</p>
<p>
This rating, unlike the previous one though is not editable, and is always recomputed after a round of contributions are accepted and synced.
</p>
</div>
<div>
<p>
<span class="underline">Evidence for a protein being a driver:</span> Having any of the below-mentioned features provide a star for a protein being a driver.
<ul class="list-decimal list-inside px-8">
<li
v-for="items in proteinFeaturesList"
:key="items"
>
{{ items }}
</li>
</ul>
</p>
<p>
This provides maximum three starts (***) for a protein which is confidently a driver.
</p>
</div>
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<li><a href="/encyclopedia">Definitions</a></li>
<li><a href="/">Crowdsourcing</a></li>
<li><a href="/about">Evidence stars</a></li>
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