Single Registration of Chemical & Biological Entities

CDD Vault supports the registration of multiple types of entities, including:

• Molecules
• Mixtures
• Nucleotides
• Amino acids
• Other

This multiple registration type selection can be enabled by CDD Support - please contact CDD Support if you wish to enable additional registration types within your Vault (s).

Once enabled, your Vault Administrator can decide which of these entity types can be registered in each Vault. Vaults can be configured either to store multiple types of entities or each each type can be stored in separate Vaults.

This article focus on how to register the different types of entities in CDD Vault.

 

Register a molecule/chemical structure record

You can register a single chemical and associated Batch data from either the Search page (using the Create a new… button) or Molecules page (using the + Create a new... button). 

A molecule can be:

• a chemical structure (with salts and/or solvents, as appropriate),
• a structureless record (a molecule record where the chemical structure in not known), or
• a simple mixture (a molecule record that simply contains 2 or more disconnected structural fragments).  

Steps for creating a new Molecule record

• After clicking the "Create a new... button, set the Registration Type to "Structure"
• Click Launch the structure editor to use Ketcher to draw a chemical structure or paste a SMILES or  MOL file in the text box
• Select the appropriate "Strip" or "Stoichiometry" radio button

• • To add salts:
    If the structure you provided contains salts or solvents drawn as part of the chemical structure, click the “Strip” radio button.

• • To enter salt or solvent information textually (not included in the structure object):
    • click the “Stoichiometry” radio button.  
    • enter the salt ratio then type the salt name.  A filtered list of salts will be displayed.  Select the appropriate salt. 
    • for solvents, enter the solvent ratio and select the solvent from the pick list.

If If the salt or solvent you need is not in the list, please contact support to have it added.

If If you want to register a pair of pure enantiomers with unknown absolute configuration, please see this article.

 

To register a chemical entity without a structure (a structureless or “No-Struct” entity):

• do not click "Launch the Structure Editor" and leave “Structure” box blank.

• fill in any data you wish to populate for your Batch fields in the “Batch Information” section. Note: The Batch Salt will be set to "Unknown Salt".
• select the desired Project and click the green “Create” button.

To register simple mixtures of disconnected chemical structure fragments:

• click Launch the Structure Editor to draw all fragments of the mixture (or paste the SMILES or MOL file in the Structure box). 
• be sure to click the “Stoichiometry” radio button.
  
  • If salts or solvents to be added, enter Salt and/or Solvent
  • If the “Salt” field is left blank, the Salt will be set to "No Salt, free base or acid".

Your registered simple mixture will look like this:

  

 

Note: If you choose Strip, the Vault will try to strip salts and solvents from the structure.  If a salt is recognized, a single entity with salt information in the salt batch field will be registered.

 

If no salts are recognized, an error message is displayed.

 

Register a mixture entity

Steps for creating a new Mixture record

• choose the "Mixture" registration type,
• launch the Mixture Editor to create your mixture, and
• enter values for the available data fields, and
• click the "Create" button.
• A placeholder mixture record can be created by leaving the mixture blank.

Within the Mixture Editor, users can look up or create mixtures:

• search for a mixture by name, and select the appropriate choice from a list of matching mixtures
• enter a mixture name or set of components, then click Parse to have the Mixture Editor create the mixture
• edit individual mixture components from scratch to create a new mixture

To look up a mixture by name, enter keyword(s) in the search box and select the desired mixture from the available options.

Once the desired mixture is found, if needed, you can then click "Launch the mixture editor" to open your selected mixture in the Mixture Editor for additions or modifications.

Another way to draw a mixture is to start with a text string, which may have been obtained from a catalog, publication, or manually typed. For example, type "ethanol (95%) in water" and click the "Parse" button.

 

 

This will activate a behind-the-scenes deep learning algorithm, which has been trained on tens of thousands of curated catalog entries. The algorithm is capable of splitting up the various parts of the text description into a hierarchy, then recreating each component using various cheminformatics technologies. Once the string is parsed, the panel switches to edit mode, with the unpacked mixture definition ready for editing. In this example, the algorithm splits the ethanol and water components, assign structures for each of them, and pulls out the ethanol concentration.

 

The most flexible way to create a mixture is to click the Edit button without entering any search term. This opens the Mixture Editor and provides a blank canvas.

The square in the middle of the editor page represents the root branch of the mixture, which is initially  empty.

The simplest of mixtures are composed of just one component, and this is the largest category in certain sources like fine chemical catalogs, most of which are just a chemical description with a purity percentage attached. Right-clicking on the square and choosing one of the 1st three menu options allows you to fully annotate this mixture component.

 

 

• Edit structure - use Ketcher to draw a chemical structure
• Edit details - use the Edit Component dialog to annotate the mixture component

• Lookup - allows you to look-up a component
• Append - adds a 2nd mixture component to the right side of the existing component
• Prepend - adds a 2nd mixture component to the left side of the existing component
• Copy - copies the existing mixture component

Another example of registering a mixture is when an active ingredient is mixed with a specific adjunct, such as a solvent. To start editing such a two-component mixture, it is necessary to create a component that is descended from the root branch. Right-click on the square and choose either the Append or Prepend menu option to add additional components to the mixture.

As above, you should:

• choose the "Mixture" registration type,
• launch the Mixture Editor to create your mixture, and
• click the "Edit" button.

Now, click on the empty square to select it, then hit the Append tool from the top menu (or right-click the empty square and choose Append from the menu). Each component can now be edited by using the tools across the top of the Mixture Editor (like Edit component, Edit structure, Lookup compound) or by right-clicking on a square and selecting the desired choice from the menu.

Once each component is fully annotated, clicking the "Use this mixture" will save the mixture entity.

 

Register a Nucleotide record

You can either register a nucleotide entity in two ways:

• Sequence
• DNA file

Sequence

Steps for creating a new Nucleotide record with the sequence

• choose the "Nucleotide" registration type,
• type or paste a nucleotide sequence into the text box, or leave it blank to create a sequence-less record.
• Enter values for the available data fields, and
• click the "Create" button.

To enter a valid sequence:

• • • • the input may be lower or upper case
      • Sequences must use standard 1- letter nucleotide codes (see the table below)
      • spaces and line breaks are ignored
      • custom/modified nucleotides can also be registered once they are created by the Vault Administrator in the new Account Management Interface. When a modified nucleotide is created by the Vault Administrator, a Unique Code is provided which can then be used when registering sequences
      • square brackets around the Code need to be used. E.g. if the modified nucleotide is “ppC”, the syntax to register a new nucleotide entity will be fo: A[ppC]CA.

Valid standard nucleotide codes:

 

DNA File

Steps for creating a new Nucleotide record using a .DNA file

 

• click the "Upload file" button and choose a .dna file

• this will store sequence, display the sequence map preview and extract the sequence from the .dna file

• fill in any entity and batch information
• select the Project where you wish to register the nucleotide entity
• click the green button "Create"

 

Register an Amino Acid record

Steps for creating a new Amino Acid record

• choose the "Amino Acid" registration type
• type or paste an amino acid sequence into the text box, or leave it blank to create a sequence-less record
• Enter values for the available data fields
• click the "Create" button

To enter a valid sequence:

• • • • Registration supports sequences of 1-letter or 3-letter amino acid codes.

      • All non-alphabetical characters, including spaces, are ignored.

      • To register a sequence of 1-letter codes:

        • • Sequence must be entirely uppercase.

          • Example: LRVILCA

      • To register a sequence of 3-letter codes:

        • • Amino acid codes must follow the capitalization format upper-lower-lower

          • Any delimiters are ignored.

          • Example 1: LeuArgValIleLeuCysAla

          • Example 2: Leu-Arg-Val-Ile-Leu-Cys-Ala

      • custom/unnatural amino acids can also be registered once they are created by the Vault Administrator in the new Account Management Interface. When a modified acid is created by the Vault Administrator, a Unique Code is provided which can then be used when registering the amino acid sequences. E.g. if a modified Amino Acid is “ppgT”, the syntax to register a new amino acid entity will be: A[ppgT]C or Ala[ppgT]Cys.

 

Valid standard amino acid codes:

3-letter:	1-letter:	3-letter:	1-letter:	3-letter:	1-letter:
Ala	A	Ile	I	Tyr	Y
Arg	R	Leu	L	Val	V
Asn	N	Lys	K	Sec	U
Asp	D	Met	M	Pyl	O
Cys	C	Phe	F	Asx	B
Gln	Q	Pro	P	Glx	Z
Glu	E	Ser	S	Xle	J
Gly	G	Thr	T	Xaa	X
His	H	Trp	W

 

Register an "Other" record

Steps for creating a new "Other" record

• choose the "Other" registration type,
• enter values for the available data fields, and
• click the "Create" button.

 

Noteworthy Tip:  the “Other” registration type is ideal for cell lines, blood/tissue samples, consumables, etc. and can be combined with a must be unique field so any unique criteria can be used. Or simply use the registration ID & batch name in your downstream workflows.