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Peptide Registration

Peptides can be registered in CDD Vault in two different ways: by structure or by sequence.

 

Peptide registration: by structure

You can register peptides containing natural amino acids with their commonly used 1- or 3-letter abbreviations. Please note that  1- and 3- letter formats can not be mixed in the same sequence, either during manual registration or in bulk registration within a single import file.

The sequences should be registered without any additional characters (no spaces or dashes) and the sequence order is from N-to-C terminal.

* Valid examples are:

AAKCLP

AlaAlaLysCysLeuPro

* Invalid examples would be:

A-A-K-C-L-P

AlaAla-LC-Leu-Pro

register_peptide.png

Limitations

There are few items you should keep in mind when registering sequences:

  • If you register a sequence in single letters, the chemical cartridge automatically converts it to 3-letter sequences and the molecule image will show "H-" at the N-terminal, and "-OH" at the C-terminal. E.g.:
    mceclip0.png
  • After around 10-15 amino acids, the structure depiction reduces in size.
  • When registering amino acid sequences as structures with 35+ amino acids, CDD Vault will not render a structure image (a message will be displayed: "Structure to large to render"). More than about 50 amino acids are not supported and may result in a registration error.  
    Although, you can use the "Structureless registration" in CDD Vault for large molecules, you can register the peptide as a sequence.  For further reading on this topic, please visit: 
    Knowledgebase article "Is it possible to add structures to structureless molecules?"

  

Tips

If you wish to keep the original character string of your sequence, you can add a batch field in your Vault, name for instance "Sequence N->C".  The character limit on a Text-type Batch Field is relatively large (65,000 characters) so you should be safe in saving the sequence of biomolecules as large as enzymes.  It could be advantageous to have this as a a required field. Any number of alternatives are possible, e.g. having a text field containing the structure in HELM notation.

When registering larger sequences, or sequences with unnatural AAs, sidechains, siRNAs, and the likes, structureless registration should work well.

In all cases, it is advisable to have a unique external identifier in case you desire to have batch-level control over your peptides. This could be either an ID by name, number, or the sequence itself.

Settings for your vault could contain following entries (Settings > Vault > Batch Fields):

mceclip3.png

An batch entry would then look something like this:

 

mceclip4.png

 

 

Tips & Tricks

In case you don't have separate batch fields for your letter sequence, you can always retrieve the originally registered sequence:
Click on your structure to open the copy box. On the bottom you will see the text "Original". Click there and the box will give you the original registration text (as MOL structure format; copy/past this into an editor and you should see your original input sequence again). 

For single compound (sequence) registration, mixing multiple annotations, as well as combining with full out drawn chemical structures, is certainly possible (again, note: single letters will be converted to 3-Letter annotation).

E.g. within the editor, you can create disulfide bridges by drawing a line from a CYS to another CYS. 

Changes to a further chemically modified amino acid are also possible. Click on an AA residue and have it expanded, followed by adding any modifications, see e.g. the below shown a His with added F and c-propyl. Of course you could simply draw the full structure from scratch.

mceclip2.png

This can be done within the Vault's Chemaxon JS editor, alternatively in e.g. Chemaxon's standalone Marvin Sketch followed by a copy/paste. SDF files created from e.g. Sketch may also be used for import via the file-import section or into the editor.

 

Peptide registration: by sequence

 

Please note: the multiple registration types can be enabled by CDD Support - please contact CDD Support if you wish to enable additional registration types within your Vault(s).

Steps for creating a peptide with the sequence

  • 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

NewAA2.png

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